Cell type-specific chromatin accessibility analysis in the mouse and human brain

References

• Klemm SL, Shipony Z, Greenleaf WJ. Chromatin accessibility and the regulatory epigenome. Nat Rev Genet. 2019;20(4):207–220.
   Google Scholar
• Zaret KS, Carroll JS. Pioneer transcription factors: establishing competence for gene expression. Genes Dev. 2011;25(21):2227–2241.
   Google Scholar
• Bell O, Tiwari VK, Thoma NH, et al. Determinants and dynamics of genome accessibility. Nat Rev Genet. 2011;12(8):554–564.
   Google Scholar
• Gallegos DA, Chan U, Chen LF, et al. Chromatin regulation of neuronal maturation and plasticity. Trends Neurosci. 2018;41(5):311–324.
   Google Scholar
• Su Y, Shin J, Zhong C, et al. Neuronal activity modifies the chromatin accessibility landscape in the adult brain. Nat Neurosci. 2017;20(3):476–483.
   Google Scholar
• Jaric I, Rocks D, Greally JM, et al. Chromatin organization in the female mouse brain fluctuates across the oestrous cycle. Nat Commun. 2019;10(1):2851.
   Google Scholar
• Maze I, Feng J, Wilkinson MB, et al. Cocaine dynamically regulates heterochromatin and repetitive element unsilencing in nucleus accumbens. Proc Natl Acad Sci U S A. 2011;108(7):3035–3040.
   Google Scholar
• Torres-Berrío A, Issler O, Parise EM, et al. Unraveling the epigenetic landscape of depression: focus on early life stress. Dialogues Clin Neurosci. 2019;21(4):341–357.
   Google Scholar
• PsychENCODE Consortium. Revealing the brain’s molecular architecture. Science. 2018;362(6420):1262–1263.
   Google Scholar
• Landt SG, Marinov GK, Kundaje A, et al. ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Res. 2012;22(9):1813–1831.
   Google Scholar
• Creyghton MP, Cheng AW, Welstead GG, et al. Histone H3K27ac separates active from poised enhancers and predicts developmental state. Proc Natl Acad Sci U S A. 2010;107(50):21931–21936.
   Google Scholar
• Heintzman ND, Stuart RK, Hon G, et al. Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat Genet. 2007;39(3):311–318.
   Google Scholar
• Heinz S, Romanoski CE, Benner C, et al. The selection and function of cell type-specific enhancers. Nat Rev Mol Cell Biol. 2015;16(3):144–154.
   Google Scholar
• Girdhar K, Hoffman GE, Jiang Y, et al. Cell-specific histone modification maps in the human frontal lobe link schizophrenia risk to the neuronal epigenome. Nat Neurosci. 2018;21(8):1126–1136.
   Google Scholar
• Kundakovic M, Jiang Y, Kavanagh DH, et al. Practical guidelines for high-resolution epigenomic profiling of nucleosomal histones in postmortem human brain tissue. Biol Psychiatry. 2017;81(2):162–170.
   Google Scholar
• Buenrostro JD, Giresi PG, Zaba LC, et al. Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nat Methods. 2013;10(12):1213–1218.
   Google Scholar
• Buenrostro JD, Wu B, Chang HY, et al. ATAC-seq: a method for assaying chromatin accessibility genome-wide. Curr Protoc Mol Biol. 2015;109:21 9 1–9.
   Google Scholar
• Milani P, Escalante-Chong R, Shelley BC, et al. Cell freezing protocol suitable for ATAC-seq on motor neurons derived from human induced pluripotent stem cells. Sci Rep. 2016;6:25474.
   Google Scholar
• Kratochvílová I, Kopečná O, Bačíková A, et al. Changes in cryopreserved cell nuclei serve as indicators of processes during freezing and thawing. Langmuir. 2019;35(23):7496–7508.
   Google Scholar
• Corces MR, Trevino AE, Hamilton EG, et al. An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. Nat Methods. 2017;14(10):959–962.
   Google Scholar
• Fernandez-Albert J, Lipinski M, Lopez-Cascales MT, et al. Immediate and deferred epigenomic signatures of in vivo neuronal activation in mouse hippocampus. Nat Neurosci. 2019;22(10):1718–1730.
   Google Scholar
• Fullard JF, Hauberg ME, Bendl J, et al. An atlas of chromatin accessibility in the adult human brain. Genome Res. 2018;28(8):1243–1252. .
   Google Scholar
• Bryois J, Garrett ME, Song L, et al. Evaluation of chromatin accessibility in prefrontal cortex of individuals with schizophrenia. Nat Commun. 2018;9(1):3121.
   Google Scholar
• Wang D, Liu S, Warrell J, et al. Comprehensive functional genomic resource and integrative model for the human brain. Science. 2018;362:6420.
   Google Scholar
• Nott A, Holtman IR, Coufal NG, et al. Brain cell type-specific enhancer-promoter interactome maps and disease-risk association. Science. 2019;366(6469):1134–1139.
   Google Scholar
• Rizzardi LF, Hickey PF, Rodriguez Diblasi V, et al. Neuronal brain-region-specific DNA methylation and chromatin accessibility are associated with neuropsychiatric trait heritability. Nat Neurosci. 2019;22(2):307–316.
   Google Scholar
• Jaric I, Rocks D, Cham H, et al. Sex and estrous cycle effects on anxiety- and depression-related phenotypes in a two-hit developmental stress model. Front Mol Neurosci. 2019;12:74.
   Google Scholar
• Kundakovic M, Gudsnuk K, Franks B, et al. Sex-specific epigenetic disruption and behavioral changes following low-dose in utero bisphenol A exposure. Proc Natl Acad Sci U S A. 2013;110(24):9956–9961.
   Google Scholar
• Gorkin DU, Barozzi I, Zhao Y, et al. An atlas of dynamic chromatin landscapes in mouse fetal development. Nature. 2020;583(7818):744–751.
   Google Scholar
• Gray LT, Yao Z, Nguyen TN, et al. Layer-specific chromatin accessibility landscapes reveal regulatory networks in adult mouse visual cortex. eLife. 2017;6:e21883.
   Google Scholar
• Liu C, Wang M, Wei X, et al. An ATAC-seq atlas of chromatin accessibility in mouse tissues. Sci Data. 2019;6(1):65.
   Google Scholar
• Marco A, Meharena HS, Dileep V, et al. Mapping the epigenomic and transcriptomic interplay during memory formation and recall in the hippocampal engram ensemble. Nat Neurosci. 2020;23(12):1606–1617.
   Google Scholar
• Mo A, Mukamel EA, Davis FP, et al. Epigenomic signatures of neuronal diversity in the mammalian brain. Neuron. 2015;86(6):1369–1384.
   Google Scholar
• Morrison KE, Cole AB, Kane PJ, et al. Pubertal adversity alters chromatin dynamics and stress circuitry in the pregnant brain. Neuropsychopharmacol. 2020;45(8):1263–1271.
   Google Scholar
• Duclot F, Kabbaj M. The role of early growth response 1 (EGR1) in brain plasticity and neuropsychiatric disorders. Front Behav Neurosci. 2017;11:35.
   Google Scholar
• Tzingounis AV, Wadiche JI. Glutamate transporters: confining runaway excitation by shaping synaptic transmission. Nat Rev Neurosci. 2007;8(12):935–947.
   Google Scholar
• Ebihara M, Ohba H, Kikuchi M, et al. Structural characterization and promoter analysis of human potassium channel Kv8. 1 (KCNV1) gene. Gene. 2004;325:89–96.
   Google Scholar
• Dedic N, Pohlmann ML, Richter JS, et al. Cross-disorder risk gene CACNA1C differentially modulates susceptibility to psychiatric disorders during development and adulthood. Mol Psychiatry. 2018;23(3):533–543.
   Google Scholar
• Sloan CA, Chan ET, Davidson JM, et al. ENCODE data at the ENCODE portal. Nucleic Acids Res. 2016;44(D1):D726–32.
   Google Scholar
• Gorkin DU, Barozzi I, Zhang Y, et al. Systematic mapping of chromatin state landscapes during mouse development. 2017:166652. https://doi.org/10.1101/166652 %J bioRxiv.
   Google Scholar
• Ernst J, Kellis M. ChromHMM: automating chromatin-state discovery and characterization. Nat Methods. 2012;9(3):215–216.
   Google Scholar
• Ong CT, Corces VG. CTCF: an architectural protein bridging genome topology and function. Nat Rev Genet. 2014;15(4):234–246.
   Google Scholar
• Yap EL, Greenberg ME. Activity-regulated transcription: bridging the gap between neural activity and behavior. Neuron. 2018;100(2):330–348.
   Google Scholar
• Cole CJ, Mercaldo V, Restivo L, et al. MEF2 negatively regulates learning-induced structural plasticity and memory formation. Nat Neurosci. 2012;15(9):1255–1264.
   Google Scholar
• Flavell SW, Cowan CW, Kim TK, et al. Activity-dependent regulation of MEF2 transcription factors suppresses excitatory synapse number. Science. 2006;311(5763):1008–1012.
   Google Scholar
• Dennis DJ, Han S, Schuurmans C. bHLH transcription factors in neural development, disease, and reprogramming. Brain Res. 2019;1705:48–65.
   Google Scholar
• Stan AD, Ghose S, Gao XM, et al. Human postmortem tissue: what quality markers matter? Brain Res. 2006;1123(1):1–11.
   Google Scholar
• Lipovich L, Dachet F, Cai J, et al. Activity-dependent human brain coding/noncoding gene regulatory networks. Genetics. 2012;192(3):1133–1148.
   Google Scholar
• Sofroniew MV, Vinters HV. Astrocytes: biology and pathology. Acta Neuropathol. 2010;119(1):7–35.
   Google Scholar
• Takizawa T, Nakashima K, Namihira M, et al. DNA methylation is a critical cell-intrinsic determinant of astrocyte differentiation in the fetal brain. Dev Cell. 2001;1(6):749–758.
   Google Scholar
• Kozlenkov A, Roussos P, Timashpolsky A, et al. Differences in DNA methylation between human neuronal and glial cells are concentrated in enhancers and non-CpG sites. Nucleic Acids Res. 2014;42(1):109–127.
   Google Scholar
• Roadmap Epigenomics C, Kundaje A, Meuleman W, et al. Integrative analysis of 111 reference human epigenomes. Nature. 2015;518(7539):317–330.
   Google Scholar
• Li H Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv:13033997 [q-bioGN]. 2013.
   Google Scholar
• Carroll TS, Liang Z, Salama R, et al. Impact of artifact removal on ChIP quality metrics in ChIP-seq and ChIP-exo data. Front Genet. 2014;5:75.
   Google Scholar
• Li Q, Brown JB, Huang H, et al. Measuring reproducibility of high-throughput experiments. Ann Appl Stat. 2011;5(3):1752–1779.
   Google Scholar
• Zhu LJ, Gazin C, Lawson ND, et al. ChIPpeakAnno: a bioconductor package to annotate ChIP-seq and ChIP-chip data. BMC Bioinf. 2010;11:237.
   Google Scholar
• Yu G, Wang L-G, Han Y, et al. clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS. 2012;16(5):284–287.
   Google Scholar
• Heinz S, Benner C, Spann N, et al. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol Cell. 2010;38(4):576–589.
   Google Scholar
• Suzuki M, Liao W, Wos F, et al. Whole-genome bisulfite sequencing with improved accuracy and cost. Genome Res. 2018;28(9):1364–1371.
   Google Scholar
• Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. %JEMBnet.journal. 2011;17(1): 3. 2011.
   Google Scholar
• Krueger F, Andrews SR. Bismark: a flexible aligner and methylation caller for bisulfite-seq applications. Bioinformatics. 2011;27(11):1571–1572.
   Google Scholar