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\begin{thebibliography}{100}
\bibitem{Ziemin-vanderPoel1991}
Ziemin-van~der Poel S, McCabe NR, Gill HJ, Espinosa R, Patel Y, Harden A,
et~al.
\newblock Identification of a gene, MLL, that spans the breakpoint in 11q23
translocations associated with human leukemias.
\newblock Proceedings of the National Academy of Sciences.
1991;88(23):10735--10739.
\bibitem{Thirman1993}
Thirman MJ, Gill HJ, Burnett RC, Mbangkollo D, McCabe NR, Kobayashi H, et~al.
\newblock Rearrangement of the MLL gene in acute lymphoblastic and acute
myeloid leukemias with 11q23 chromosomal translocations.
\newblock New England Journal of Medicine. 1993;329(13):909--914.
\bibitem{Li2014a}
Li BE, Ernst P.
\newblock Two decades of leukemia oncoprotein epistasis: the MLL1 paradigm for
epigenetic deregulation in leukemia.
\newblock Exp Hematol. 2014 Dec;42(12):995--1012.
\newblock Available from: \url{http://dx.doi.org/10.1016/j.exphem.2014.09.006}.
\bibitem{VanderBurg1999}
Van~der Burg M, Beverloo H, Langerak A, Wijsman J, Van~Drunen E, Slater R,
et~al.
\newblock Rapid and sensitive detection of all types of MLL gene translocations
with a single FISH probe set.
\newblock Leukemia (08876924). 1999;13(12).
\bibitem{Slany2016}
Slany RK.
\newblock The molecular mechanics of mixed lineage leukemia.
\newblock Oncogene. 2016;35(40):5215--5223.
\bibitem{Kobayashi1993}
Kobayashi H, Thirman M, Gill H, Fernald A, Diaz M, Le~Beau M, et~al.
\newblock Heterogeneity of breakpoints of 11q23 rearrangements in hematologic
malignancies identified with fluorescence in situ hybridization.
\newblock Blood. 1993;82(2):547--551.
\bibitem{Tkachuk1992}
Tkachuk DC, Kohler S, Cleary ML.
\newblock Involvement of a homolog of Drosophila trithorax by 11q23 chromosomal
translocations in acute leukemias.
\newblock Cell. 1992;71(4):691--700.
\bibitem{Djabali1992}
Djabali M, Selleri L, Parry P, Bower M, Young BD, Evans GA.
\newblock A trithorax--like gene is interrupted by chromosome 11q23
translocations in acute leukaemias.
\newblock Nature genetics. 1992;2(2):113--118.
\bibitem{Rowley1973}
Rowley JD.
\newblock A new consistent chromosomal abnormality in chronic myelogenous
leukaemia identified by quinacrine fluorescence and Giemsa staining.
\newblock Nature. 1973;243(5405):290--293.
\bibitem{Sorensen1994}
Sorensen P, Chen Cs, Smith FO, Arthur DC, Domer PH, Bernstein ID, et~al.
\newblock Molecular rearrangements of the MLL gene are present in most cases of
infant acute myeloid leukemia and are strongly correlated with monocytic or
myelomonocytic phenotypes.
\newblock Journal of Clinical Investigation. 1994;93(1):429.
\bibitem{Balgobind2009}
Balgobind BV, Raimondi SC, Harbott J, Zimmermann M, Alonzo TA, Auvrignon A,
et~al.
\newblock Novel prognostic subgroups in childhood 11q23/MLL-rearranged acute
myeloid leukemia: results of an international retrospective study.
\newblock Blood. 2009 Sep;114:2489--2496.
\bibitem{Bolouri2017}
Bolouri H, Farrar JE, Triche~Jr T, Ries RE, Lim EL, Alonzo TA, et~al.
\newblock The molecular landscape of pediatric acute myeloid leukemia reveals
recurrent structural alterations and age-specific mutational interactions.
\newblock Nature medicine. 2017;.
\bibitem{Super1993}
Super H, McCabe NR, Thirman MJ, Larson RA, Le~Beau MM, Pedersen-Bjergaard J,
et~al.
\newblock Rearrangements of the MLL gene in therapy-related acute myeloid
leukemia in patients previously treated with agents targeting
DNA-topoisomerase II.
\newblock Blood. 1993;82(12):3705--3711.
\bibitem{Arber2016}
Arber DA, Orazi A, Hasserjian R, Thiele J, Borowitz MJ, Le~Beau MM, et~al.
\newblock The 2016 revision to the World Health Organization classification of
myeloid neoplasms and acute leukemia.
\newblock Blood. 2016 May;127:2391--2405.
\bibitem{He2010}
He N, Liu M, Hsu J, Xue Y, Chou S, Burlingame A, et~al.
\newblock HIV-1 Tat and host AFF4 recruit two transcription elongation factors
into a bifunctional complex for coordinated activation of HIV-1
transcription.
\newblock Molecular cell. 2010 May;38:428--438.
\bibitem{Lin2010}
Lin C, Smith ER, Takahashi H, Lai KC, Martin-Brown S, Florens L, et~al.
\newblock AFF4, a component of the ELL/P-TEFb elongation complex and a shared
subunit of MLL chimeras, can link transcription elongation to leukemia.
\newblock Molecular cell. 2010;37(3):429--437.
\bibitem{Mohan2010}
Mohan M, Lin C, Guest E, Shilatifard A.
\newblock Licensed to elongate: a molecular mechanism for MLL-based
leukaemogenesis.
\newblock Nature reviews Cancer. 2010 Oct;10:721--728.
\bibitem{Calvanese2019}
Calvanese V, Nguyen AT, Bolan TJ, Vavilina A, Su T, Lee LK, et~al.
\newblock MLLT3 governs human haematopoietic stem-cell self-renewal and
engraftment.
\newblock Nature. 2019 Nov;.
\bibitem{Somervaille2009}
Somervaille TCP, Matheny CJ, Spencer GJ, Iwasaki M, Rinn JL, Witten DM, et~al.
\newblock Hierarchical maintenance of MLL myeloid leukemia stem cells employs a
transcriptional program shared with embryonic rather than adult stem cells.
\newblock Cell Stem Cell. 2009 Feb;4(2):129--140.
\newblock Available from: \url{http://dx.doi.org/10.1016/j.stem.2008.11.015}.
\bibitem{Krivtsov2013}
Krivtsov AV, Figueroa ME, Sinha AU, Stubbs MC, Feng Z, Valk PJM, et~al.
\newblock Cell of origin determines clinically relevant subtypes of
MLL-rearranged AML.
\newblock Leukemia. 2013 Apr;27(4):852--860.
\newblock Available from: \url{http://dx.doi.org/10.1038/leu.2012.363}.
\bibitem{Stavropoulou2016}
Stavropoulou V, Kaspar S, Brault L, Sanders MA, Juge S, Morettini S, et~al.
\newblock MLL-AF9 Expression in Hematopoietic Stem Cells Drives a Highly
Invasive AML Expressing EMT-Related Genes Linked to Poor Outcome.
\newblock Cancer Cell. 2016 Jun;Available from:
\url{http://dx.doi.org/10.1016/j.ccell.2016.05.011}.
\bibitem{George2016}
George J, Uyar A, Young K, Kuffler L, Waldron-Francis K, Marquez E, et~al.
\newblock Leukaemia cell of origin identified by chromatin landscape of bulk
tumour cells.
\newblock Nature communications. 2016 Jul;7:12166.
\bibitem{Dick2005}
Dick JE, Lapidot T.
\newblock Biology of normal and acute myeloid leukemia stem cells.
\newblock Int J Hematol. 2005 Dec;82(5):389--396.
\newblock Available from: \url{http://dx.doi.org/10.1532/IJH97.05144}.
\bibitem{Krivtsov2006}
Krivtsov AV, Twomey D, Feng Z, Stubbs MC, Wang Y, Faber J, et~al.
\newblock Transformation from committed progenitor to leukaemia stem cell
initiated by MLL-AF9.
\newblock Nature. 2006 Aug;442(7104):818--822.
\newblock Available from: \url{http://dx.doi.org/10.1038/nature04980}.
\bibitem{Somervaille2006}
Somervaille TCP, Cleary ML.
\newblock {Identification and characterization of leukemia stem cells in murine
MLL-AF9 acute myeloid leukemia.}
\newblock Cancer Cell. 2006 Oct;10(4):257--68.
\newblock Available from: \url{http://www.ncbi.nlm.nih.gov/pubmed/17045204}.
\bibitem{Johnson1925}
Johnson TB, Coghill RD.
\newblock Researches on pyrimidines C111. The discovery of 5-methyl-cytosine in
tuberculinic acid, the nucleic acid of the tubercle bacillus.
\newblock Journal of the American Chemical Society. 1925;47(11):2838--2844.
\newblock Available from: \url{https://doi.org/10.1021/ja01688a030}.
\bibitem{Cohn1951}
Cohn WE.
\newblock The Isolation and Identification of Desoxy-5-methylcytidylic Acid
from Thymus Nucleic Acid1.
\newblock J Am Chem Soc. 1951 Apr;73(4):1539--1541.
\newblock Available from: \url{https://doi.org/10.1021/ja01148a039}.
\bibitem{Dominissini2012}
Dominissini D, Moshitch-Moshkovitz S, Schwartz S, Salmon-Divon M, Ungar L,
Osenberg S, et~al.
\newblock Topology of the human and mouse m6A RNA methylomes revealed by
m6A-seq.
\newblock Nature. 2012 Apr;485:201--206.
\bibitem{Ji2018}
Ji P, Wang X, Xie N, Li Y.
\newblock N6-Methyladenosine in RNA and DNA: An Epitranscriptomic and
Epigenetic Player Implicated in Determination of Stem Cell Fate.
\newblock Stem cells international. 2018;2018:3256524.
\bibitem{Schuebeler2015}
Schübeler D.
\newblock Function and information content of DNA methylation.
\newblock Nature. 2015 Jan;517:321--326.
\bibitem{Luo2018}
Luo C, Hajkova P, Ecker JR.
\newblock Dynamic DNA methylation: In the right place at the right time.
\newblock Science (New York, NY). 2018 Sep;361:1336--1340.
\bibitem{Lyko2018}
Lyko F.
\newblock The DNA methyltransferase family: a versatile toolkit for epigenetic
regulation.
\newblock Nature reviews Genetics. 2018 Feb;19:81--92.
\bibitem{Pastor2013}
Pastor WA, Aravind L, Rao A.
\newblock TETonic shift: biological roles of TET proteins in DNA demethylation
and transcription.
\newblock Nature reviews Molecular cell biology. 2013 Jun;14:341--356.
\bibitem{Shen2014a}
Shen L, Song CX, He C, Zhang Y.
\newblock Mechanism and function of oxidative reversal of DNA and RNA
methylation.
\newblock Annual review of biochemistry. 2014;83:585--614.
\bibitem{Plongthongkum2014}
Plongthongkum N, Diep DH, Zhang K.
\newblock Advances in the profiling of DNA modifications: cytosine methylation
and beyond.
\newblock Nature reviews Genetics. 2014 Oct;15:647--661.
\bibitem{Wijst2015}
van~der Wijst MGP, Venkiteswaran M, Chen H, Xu GL, Plösch T, Rots MG.
\newblock Local chromatin microenvironment determines DNMT activity: from DNA
methyltransferase to DNA demethylase or DNA dehydroxymethylase.
\newblock Epigenetics. 2015;10:671--676.
\bibitem{Meissner2005}
Meissner A, Gnirke A, Bell GW, Ramsahoye B, Lander ES, Jaenisch R.
\newblock {Reduced representation bisulfite sequencing for comparative
high-resolution DNA methylation analysis.}
\newblock Nucleic acids research. 2005 Jan;33(18):5868--77.
\newblock Available from:
\url{http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1258174\&tool=pmcentrez\&rendertype=abstract}.
\bibitem{Mulqueen2018}
Mulqueen RM, Pokholok D, Norberg SJ, Torkenczy KA, Fields AJ, Sun D, et~al.
\newblock Highly scalable generation of DNA methylation profiles in single
cells.
\newblock Nature biotechnology. 2018 Apr;.
\bibitem{Wreczycka2017}
Wreczycka K, Gosdschan A, Yusuf D, Grüning B, Assenov Y, Akalin A.
\newblock Strategies for analyzing bisulfite sequencing data.
\newblock Journal of biotechnology. 2017 Nov;261:105--115.
\bibitem{Xing2018}
Xing X, Zhang B, Li D, Wang T.
\newblock Comprehensive Whole DNA Methylome Analysis by Integrating MeDIP-seq
and MRE-seq.
\newblock Methods in molecular biology (Clifton, NJ). 2018;1708:209--246.
\bibitem{Kioussis1983}
Kioussis D, Vanin E, deLange T, Flavell RA, Grosveld FG.
\newblock Beta-globin gene inactivation by DNA translocation in gamma
beta-thalassaemia.
\newblock Nature. 1983;306:662--666.
\bibitem{Bergman2013}
Bergman Y, Cedar H.
\newblock DNA methylation dynamics in health and disease.
\newblock Nat Struct Mol Biol. 2013 Mar;20(3):274--281.
\newblock Available from: \url{http://dx.doi.org/10.1038/nsmb.2518}.
\bibitem{Rodriguez-Paredes2011}
Rodr\'{\i}guez-Paredes M, Esteller M.
\newblock {Cancer epigenetics reaches mainstream oncology.}
\newblock Nature medicine. 2011 Mar;17(3):330--9.
\newblock Available from: \url{http://www.ncbi.nlm.nih.gov/pubmed/21386836}.
\bibitem{Vidal2017}
Vidal E, Sayols S, Moran S, Guillaumet-Adkins A, Schroeder MP, Royo R, et~al.
\newblock A DNA methylation map of human cancer at single base-pair resolution.
\newblock Oncogene. 2017 Oct;36:5648--5657.
\bibitem{Eriksson2015}
Eriksson A, Lennartsson A, Lehmann S.
\newblock Epigenetic aberrations in acute myeloid leukemia: Early key events
during leukemogenesis.
\newblock Exp Hematol. 2015 Aug;43(8):609--624.
\newblock Available from: \url{http://dx.doi.org/10.1016/j.exphem.2015.05.009}.
\bibitem{TCGAC2013}
{Cancer Genome Atlas Research Network}.
\newblock Genomic and epigenomic landscapes of adult de novo acute myeloid
leukemia.
\newblock N Engl J Med. 2013 May;368(22):2059--2074.
\newblock Available from: \url{http://dx.doi.org/10.1056/NEJMoa1301689}.
\bibitem{Figueroa2010}
Figueroa ME, Lugthart S, Li Y, Erpelinck-Verschueren C, Deng X, Christos PJ,
et~al.
\newblock DNA methylation signatures identify biologically distinct subtypes in
acute myeloid leukemia.
\newblock Cancer cell. 2010 Jan;17:13--27.
\bibitem{Akalin2012a}
Akalin A, Garrett-Bakelman FE, Kormaksson M, Busuttil J, Zhang L, Khrebtukova
I, et~al.
\newblock Base-pair resolution DNA methylation sequencing reveals profoundly
divergent epigenetic landscapes in acute myeloid leukemia.
\newblock PLoS genetics. 2012;8:e1002781.
\bibitem{Challen2014}
Challen GA, Sun D, Mayle A, Jeong M, Luo M, Rodriguez B, et~al.
\newblock Dnmt3a and Dnmt3b have overlapping and distinct functions in
hematopoietic stem cells.
\newblock Cell stem cell. 2014 Sep;15:350--364.
\bibitem{Cole2017}
Cole CB, Russler-Germain DA, Ketkar S, Verdoni AM, Smith AM, Bangert CV, et~al.
\newblock Haploinsufficiency for DNA methyltransferase 3A predisposes
hematopoietic cells to myeloid malignancies.
\newblock The Journal of clinical investigation. 2017 Oct;127:3657--3674.
\bibitem{Weinberg2019}
Weinberg DN, Papillon-Cavanagh S, Chen H, Yue Y, Chen X, Rajagopalan KN, et~al.
\newblock The histone mark H3K36me2 recruits DNMT3A and shapes the intergenic
DNA methylation landscape.
\newblock Nature. 2019 Sep;.
\bibitem{Im2014}
Im AP, Sehgal AR, Carroll MP, Smith BD, Tefferi A, Johnson DE, et~al.
\newblock DNMT3A and IDH mutations in acute myeloid leukemia and other myeloid
malignancies: associations with prognosis and potential treatment strategies.
\newblock Leukemia. 2014 Sep;28:1774--1783.
\bibitem{Raffel2017}
Raffel S, Falcone M, Kneisel N, Hansson J, Wang W, Lutz C, et~al.
\newblock BCAT1 restricts αKG levels in AML stem cells leading to IDHmut-like
DNA hypermethylation.
\newblock Nature. 2017 Nov;551:384--388.
\bibitem{Rampal2014}
Rampal R, Alkalin A, Madzo J, Vasanthakumar A, Pronier E, Patel J, et~al.
\newblock DNA hydroxymethylation profiling reveals that WT1 mutations result in
loss of TET2 function in acute myeloid leukemia.
\newblock Cell reports. 2014 Dec;9:1841--1855.
\bibitem{Lorsbach2003}
Lorsbach R, Moore J, Mathew S, Raimondi S, Mukatira S, Downing J.
\newblock TET1, a member of a novel protein family, is fused to MLL in acute
myeloid leukemia containing the t (10; 11)(q22; q23).
\newblock Leukemia. 2003;17(3):637--641.
\bibitem{Moran-Crusio2011}
Moran-Crusio K, Reavie L, Shih A, Abdel-Wahab O, Ndiaye-Lobry D, Lobry C,
et~al.
\newblock Tet2 loss leads to increased hematopoietic stem cell self-renewal and
myeloid transformation.
\newblock Cancer cell. 2011 Jul;20:11--24.
\bibitem{Solary2014}
Solary E, Bernard OA, Tefferi A, Fuks F, Vainchenker W.
\newblock The Ten-Eleven Translocation-2 (TET2) gene in hematopoiesis and
hematopoietic diseases.
\newblock Leukemia. 2014 Mar;28:485--496.
\bibitem{Sonnet2014}
Sonnet M, Claus R, Becker N, Zucknick M, Petersen J, Lipka DB, et~al.
\newblock Early aberrant DNA methylation events in a mouse model of acute
myeloid leukemia.
\newblock Genome medicine. 2014;6:34.
\bibitem{Schoofs2013a}
Schoofs T, Berdel WE, Müller-Tidow C.
\newblock Origins of aberrant DNA methylation in acute myeloid leukemia.
\newblock Leukemia. 2013 Aug;Available from:
\url{http://dx.doi.org/10.1038/leu.2013.242}.
\bibitem{Sanyal2012}
Sanyal A, Lajoie BR, Jain G, Dekker J.
\newblock The long-range interaction landscape of gene promoters.
\newblock Nature. 2012;489(7414):109.
\bibitem{Mifsud2015}
Mifsud B, Tavares-Cadete F, Young AN, Sugar R, Schoenfelder S, Ferreira L,
et~al.
\newblock Mapping long-range promoter contacts in human cells with
high-resolution capture Hi-C.
\newblock Nature genetics. 2015 Jun;47:598--606.
\bibitem{Fulco2016}
Fulco CP, Munschauer M, Anyoha R, Munson G, Grossman SR, Perez EM, et~al.
\newblock Systematic mapping of functional enhancer-promoter connections with
CRISPR interference.
\newblock Science (New York, NY). 2016 Nov;354:769--773.
\bibitem{Lettice2003}
Lettice LA, Heaney SJH, Purdie LA, Li L, de~Beer P, Oostra BA, et~al.
\newblock A long-range Shh enhancer regulates expression in the developing limb
and fin and is associated with preaxial polydactyly.
\newblock Human molecular genetics. 2003 Jul;12:1725--1735.
\bibitem{Hughes2014}
Hughes JR, Roberts N, McGowan S, Hay D, Giannoulatou E, Lynch M, et~al.
\newblock Analysis of hundreds of cis-regulatory landscapes at high resolution
in a single, high-throughput experiment.
\newblock Nature genetics. 2014;46(2):205.
\bibitem{Bertolino2016}
Bertolino E, Reinitz J, Manu.
\newblock The analysis of novel distal Cebpa enhancers and silencers using a
transcriptional model reveals the complex regulatory logic of hematopoietic
lineage specification.
\newblock Developmental biology. 2016 May;413:128--144.
\bibitem{Javierre2016}
Javierre BM, Burren OS, Wilder SP, Kreuzhuber R, Hill SM, Sewitz S, et~al.
\newblock Lineage-Specific Genome Architecture Links Enhancers and Non-coding
Disease Variants to Target Gene Promoters.
\newblock Cell. 2016 Nov;167:1369--1384.e19.
\bibitem{Arensbergen2014}
van Arensbergen J, van Steensel B, Bussemaker HJ.
\newblock In search of the determinants of enhancer--promoter interaction
specificity.
\newblock Trends in cell biology. 2014;24(11):695--702.
\bibitem{Drissen2004}
Drissen R, Palstra RJ, Gillemans N, Splinter E, Grosveld F, Philipsen S, et~al.
\newblock The active spatial organization of the beta-globin locus requires the
transcription factor EKLF.
\newblock Genes \& development. 2004 Oct;18:2485--2490.
\bibitem{Vakoc2005}
Vakoc CR, Letting DL, Gheldof N, Sawado T, Bender MA, Groudine M, et~al.
\newblock Proximity among distant regulatory elements at the beta-globin locus
requires GATA-1 and FOG-1.
\newblock Molecular cell. 2005 Feb;17:453--462.
\bibitem{Jin2013}
Jin F, Li Y, Dixon JR, Selvaraj S, Ye Z, Lee AY, et~al.
\newblock A high-resolution map of the three-dimensional chromatin interactome
in human cells.
\newblock Nature. 2013 Nov;503:290--294.
\bibitem{Haarhuis2017}
Haarhuis JHI, van~der Weide RH, Blomen VA, Yáñez-Cuna JO, Amendola M, van
Ruiten MS, et~al.
\newblock The Cohesin Release Factor WAPL Restricts Chromatin Loop Extension.
\newblock Cell. 2017 May;169:693--707.e14.
\bibitem{Kornberg2005}
Kornberg RD.
\newblock Mediator and the mechanism of transcriptional activation.
\newblock Trends in biochemical sciences. 2005 May;30:235--239.
\bibitem{Robinson2016}
Robinson PJ, Trnka MJ, Bushnell DA, Davis RE, Mattei PJ, Burlingame AL, et~al.
\newblock Structure of a Complete Mediator-RNA Polymerase II Pre-Initiation
Complex.
\newblock Cell. 2016 Sep;166:1411--1422.e16.
\bibitem{Kaiser1996}
Kaiser K, Meisterernst M.
\newblock The human general co-factors.
\newblock Trends in biochemical sciences. 1996 Sep;21:342--345.
\bibitem{Ogryzko1996}
Ogryzko VV, Schiltz RL, Russanova V, Howard BH, Nakatani Y.
\newblock The transcriptional coactivators p300 and CBP are histone
acetyltransferases.
\newblock Cell. 1996 Nov;87:953--959.
\bibitem{Spencer1997}
Spencer TE, Jenster G, Burcin MM, Allis CD, Zhou J, Mizzen CA, et~al.
\newblock Steroid receptor coactivator-1 is a histone acetyltransferase.
\newblock Nature. 1997 Sep;389:194--198.
\bibitem{Hirose2007}
Hirose Y, Ohkuma Y.
\newblock Phosphorylation of the C-terminal domain of RNA polymerase II plays
central roles in the integrated events of eucaryotic gene expression.
\newblock Journal of biochemistry. 2007 May;141:601--608.
\bibitem{Kim2010}
Kim TK, Hemberg M, Gray JM, Costa AM, Bear DM, Wu J, et~al.
\newblock Widespread transcription at neuronal activity-regulated enhancers.
\newblock Nature. 2010 May;465(7295):182--187.
\newblock Available from: \url{http://dx.doi.org/10.1038/nature09033}.
\bibitem{DeSanta2010}
{De Santa} F, Barozzi I, Mietton F, Ghisletti S, Polletti S, Tusi BK, et~al.
\newblock A large fraction of extragenic RNA pol II transcription sites overlap
enhancers.
\newblock PLoS Biol. 2010 May;8(5):e1000384.
\newblock Available from: \url{http://dx.doi.org/10.1371/journal.pbio.1000384}.
\bibitem{Zhu2013a}
Zhu Y, Sun L, Chen Z, Whitaker JW, Wang T, Wang W.
\newblock Predicting enhancer transcription and activity from chromatin
modifications.
\newblock Nucleic Acids Res. 2013 Dec;41(22):10032--10043.
\newblock Available from: \url{http://dx.doi.org/10.1093/nar/gkt826}.
\bibitem{Koch2011}
Koch F, Fenouil R, Gut M, Cauchy P, Albert TK, Zacarias-Cabeza J, et~al.
\newblock Transcription initiation platforms and GTF recruitment at
tissue-specific enhancers and promoters.
\newblock Nature structural \& molecular biology. 2011 Jul;18:956--963.
\bibitem{Andersson2014}
Andersson R, Gebhard C, Miguel-Escalada I, Hoof I, Bornholdt J, Boyd M, et~al.
\newblock An atlas of active enhancers across human cell types and tissues.
\newblock Nature. 2014 Mar;507(7493):455--461.
\newblock Available from: \url{http://dx.doi.org/10.1038/nature12787}.
\bibitem{Core2014}
Core LJ, Martins AL, Danko CG, Waters CT, Siepel A, Lis JT.
\newblock Analysis of nascent RNA identifies a unified architecture of
initiation regions at mammalian promoters and enhancers.
\newblock Nature genetics. 2014 Dec;46:1311--1320.
\bibitem{Wang2011}
Wang D, Garcia-Bassets I, Benner C, Li W, Su X, Zhou Y, et~al.
\newblock Reprogramming transcription by distinct classes of enhancers
functionally defined by eRNA.
\newblock Nature. 2011 May;474:390--394.
\bibitem{Li2013a}
Li W, Notani D, Ma Q, Tanasa B, Nunez E, Chen AY, et~al.
\newblock Functional roles of enhancer RNAs for oestrogen-dependent
transcriptional activation.
\newblock Nature. 2013 Jun;498(7455):516--520.
\newblock Available from: \url{http://dx.doi.org/10.1038/nature12210}.
\bibitem{Kaikkonen2013}
Kaikkonen MU, Spann NJ, Heinz S, Romanoski CE, Allison KA, Stender JD, et~al.
\newblock Remodeling of the enhancer landscape during macrophage activation is
coupled to enhancer transcription.
\newblock Molecular cell. 2013 Aug;51:310--325.
\bibitem{Aguilo2016}
Aguilo F, Li S, Balasubramaniyan N, Sancho A, Benko S, Zhang F, et~al.
\newblock Deposition of 5-Methylcytosine on Enhancer RNAs Enables the
Coactivator Function of PGC-1$\alpha$.
\newblock Cell reports. 2016 Jan;14:479--492.
\bibitem{Lam2014}
Lam MTY, Li W, Rosenfeld MG, Glass CK.
\newblock Enhancer RNAs and regulated transcriptional programs.
\newblock Trends Biochem Sci. 2014 Apr;39(4):170--182.
\newblock Available from: \url{http://dx.doi.org/10.1016/j.tibs.2014.02.007}.
\bibitem{Arner2015}
Arner E, Daub CO, Vitting-Seerup K, Andersson R, Lilje B, Drabl{\o}s F, et~al.
\newblock Gene regulation. Transcribed enhancers lead waves of coordinated
transcription in transitioning mammalian cells.
\newblock Science. 2015 Feb;347(6225):1010--1014.
\newblock Available from: \url{http://dx.doi.org/10.1126/science.1259418}.
\bibitem{Su2014a}
Su X, Malouf GG, Chen Y, Zhang J, Yao H, Valero V, et~al.
\newblock Comprehensive analysis of long non-coding RNAs in human breast cancer
clinical subtypes.
\newblock Oncotarget. 2014 Oct;5:9864--9876.
\bibitem{Chen2017d}
Chen H, Du G, Song X, Li L.
\newblock Non-coding Transcripts from Enhancers: New Insights into Enhancer
Activity and Gene Expression Regulation.
\newblock Genomics, proteomics \& bioinformatics. 2017 Jun;15:201--207.
\bibitem{Fong2001}
Fong YW, Zhou Q.
\newblock Stimulatory effect of splicing factors on transcriptional elongation.
\newblock Nature. 2001;414:929--933.
\bibitem{Austenaa2015}
Austenaa LMI, Barozzi I, Simonatto M, Masella S, {Della Chiara} G, Ghisletti S,
et~al.
\newblock Transcription of Mammalian cis-Regulatory Elements Is Restrained by
Actively Enforced Early Termination.
\newblock Mol Cell. 2015 Nov;60(3):460--474.
\newblock Available from: \url{http://dx.doi.org/10.1016/j.molcel.2015.09.018}.
\bibitem{CQuaresma2016}
C~Quaresma AJ, Bugai A, Barboric M.
\newblock Cracking the control of RNA polymerase II elongation by 7SK snRNP and
P-TEFb.
\newblock Nucleic acids research. 2016 Sep;44:7527--7539.
\bibitem{Flynn2016}
Flynn RA, Do BT, Rubin AJ, Calo E, Lee B, Kuchelmeister H, et~al.
\newblock 7SK-BAF axis controls pervasive transcription at enhancers.
\newblock Nature structural \& molecular biology. 2016 Mar;23:231--238.
\bibitem{Meng2014}
Meng FL, Du Z, Federation A, Hu J, Wang Q, Kieffer-Kwon KR, et~al.
\newblock Convergent transcription at intragenic super-enhancers targets
AID-initiated genomic instability.
\newblock Cell. 2014 Dec;159:1538--1548.
\bibitem{Ernst2010}
Ernst J, Kellis M.
\newblock Discovery and characterization of chromatin states for systematic
annotation of the human genome.
\newblock Nat Biotechnol. 2010 Aug;28(8):817--825.
\newblock Available from: \url{http://dx.doi.org/10.1038/nbt.1662}.
\bibitem{CaloWysocka2013}
Calo E, Wysocka J.
\newblock Modification of enhancer chromatin: what, how, and why?
\newblock Mol Cell. 2013 Mar;49(5):825--837.
\newblock Available from: \url{http://dx.doi.org/10.1016/j.molcel.2013.01.038}.
\bibitem{Heinz2015}
Heinz S, Romanoski CE, Benner C, Glass CK.
\newblock The selection and function of cell type-specific enhancers.
\newblock Nat Rev Mol Cell Biol. 2015 Feb;Available from:
\url{http://dx.doi.org/10.1038/nrm3949}.
\bibitem{Lim2018}
Lim LWK, Chung HH, Chong YL, Lee NK.
\newblock A survey of recently emerged genome-wide computational enhancer
predictor tools.
\newblock Computational biology and chemistry. 2018 Jun;74:132--141.
\bibitem{Lara-Astiaso2014}
Lara-Astiaso D, Weiner A, Lorenzo-Vivas E, Zaretsky I, Jaitin DA, David E,
et~al.
\newblock Chromatin state dynamics during blood formation.
\newblock Science. 2014 Aug;345(6199):943--949.
\newblock Available from: \url{http://dx.doi.org/10.1126/science.1256271}.
\bibitem{Ulirsch2019}
Ulirsch JC, Lareau CA, Bao EL, Ludwig LS, Guo MH, Benner C, et~al.
\newblock Interrogation of human hematopoiesis at single-cell and
single-variant resolution.
\newblock Nature genetics. 2019 Mar;.
\bibitem{Bresnick2019}
Bresnick EH, Johnson KD.
\newblock Blood disease-causing and -suppressing transcriptional enhancers:
general principles and and GATA2 mechanisms.
\newblock Blood advances. 2019 Jul;3:2045--2056.
\bibitem{Zuber2011}
Zuber J, Shi J, Wang E, Rappaport AR, Herrmann H, Sison Ea, et~al.
\newblock {RNAi screen identifies Brd4 as a therapeutic target in acute myeloid
leukaemia.}
\newblock Nature. 2011 Oct;478(7370):524--8.
\newblock Available from: \url{http://www.ncbi.nlm.nih.gov/pubmed/21814200}.
\bibitem{Shi2013}
Shi J, Whyte WA, Zepeda-Mendoza CJ, Milazzo JP, Shen C, Roe JS, et~al.
\newblock Role of SWI/SNF in acute leukemia maintenance and enhancer-mediated
Myc regulation.
\newblock Genes \& development. 2013 Dec;27:2648--2662.
\bibitem{Bahr2018}
Bahr C, von Paleske L, Uslu VV, Remeseiro S, Takayama N, Ng SW, et~al.
\newblock A Myc enhancer cluster regulates normal and leukaemic haematopoietic
stem cell hierarchies.
\newblock Nature. 2018 Jan;553:515--520.
\bibitem{Rosenbauer2004}
Rosenbauer F, Wagner K, Kutok JL, Iwasaki H, Le~Beau MM, Okuno Y, et~al.
\newblock Acute myeloid leukemia induced by graded reduction of a
lineage-specific transcription factor, PU. 1.
\newblock Nature genetics. 2004;36(6):624.
\bibitem{Metcalf2006}
Metcalf D, Dakic A, Mifsud S, Di~Rago L, Wu L, Nutt S.
\newblock Inactivation of PU.1 in adult mice leads to the development of
myeloid leukemia.
\newblock Proceedings of the National Academy of Sciences of the United States
of America. 2006 Jan;103:1486--1491.
\bibitem{Will2015}
Will B, Vogler TO, Narayanagari S, Bartholdy B, Todorova TI, {da Silva
Ferreira} M, et~al.
\newblock Minimal PU.1 reduction induces a preleukemic state and promotes
development of acute myeloid leukemia.
\newblock Nat Med. 2015 Oct;21(10):1172--1181.
\newblock Available from: \url{http://dx.doi.org/10.1038/nm.3936}.
\bibitem{Corces2016}
Corces MR, Buenrostro JD, Wu B, Greenside PG, Chan SM, Koenig JL, et~al.
\newblock Lineage-specific and single-cell chromatin accessibility charts human
hematopoiesis and leukemia evolution.
\newblock Nat Genet. 2016 Aug;Available from:
\url{http://dx.doi.org/10.1038/ng.3646}.
\bibitem{Mansour2014}
Mansour MR, Abraham BJ, Anders L, Berezovskaya A, Gutierrez A, Durbin AD,
et~al.
\newblock Oncogene regulation. An oncogenic super-enhancer formed through
somatic mutation of a noncoding intergenic element.
\newblock Science. 2014 Dec;346(6215):1373--1377.
\newblock Available from: \url{http://dx.doi.org/10.1126/science.1259037}.
\bibitem{Vahedi2015}
Vahedi G, Kanno Y, Furumoto Y, Jiang K, Parker SCJ, Erdos MR, et~al.
\newblock Super-enhancers delineate disease-associated regulatory nodes in T
cells.
\newblock Nature. 2015 Feb;Available from:
\url{http://dx.doi.org/10.1038/nature14154}.
\bibitem{Huang2019}
Huang Y, Mouttet B, Warnatz HJ, Risch T, Rietmann F, Frommelt F, et~al.
\newblock The Leukemogenic TCF3-HLF Complex Rewires Enhancers Driving Cellular
Identity and Self-Renewal Conferring EP300 Vulnerability.
\newblock Cancer cell. 2019 Nov;.
\bibitem{Yamazaki2014}
Yamazaki H, Suzuki M, Otsuki A, Shimizu R, Bresnick EH, Engel JD, et~al.
\newblock A remote GATA2 hematopoietic enhancer drives leukemogenesis in
inv(3)(q21;q26) by activating EVI1 expression.
\newblock Cancer Cell. 2014 Apr;25(4):415--427.
\newblock Available from: \url{http://dx.doi.org/10.1016/j.ccr.2014.02.008}.
\bibitem{Groeschel2014}
Gr{\"{o}}schel S, Sanders MA, Hoogenboezem R, {de Wit} E, Bouwman BAM,
Erpelinck C, et~al.
\newblock A single oncogenic enhancer rearrangement causes concomitant EVI1 and
GATA2 deregulation in leukemia.
\newblock Cell. 2014 Apr;157(2):369--381.
\newblock Available from: \url{http://dx.doi.org/10.1016/j.cell.2014.02.019}.
\bibitem{Broeske2009}
Br{\"{o}}ske AM, Vockentanz L, Kharazi S, Huska MR, Mancini E, Scheller M,
et~al.
\newblock DNA methylation protects hematopoietic stem cell multipotency from
myeloerythroid restriction.
\newblock Nat Genet. 2009 Nov;41(11):1207--1215.
\newblock Available from: \url{http://dx.doi.org/10.1038/ng.463}.
\bibitem{Vockentanz2010}
Vockentanz L, Br\"{o}ske AM, Rosenbauer F.
\newblock {Uncovering a unique role for DNA methylation in hematopoietic and
leukemic stem cells.}
\newblock Cell cycle (Georgetown, Tex). 2010 Feb;9(4):640--1.
\newblock Available from: \url{http://www.ncbi.nlm.nih.gov/pubmed/20107327}.
\bibitem{Vockentanz2011}
Vockentanz L.
\newblock {Leukemia Stem Cell Fates are Determined by DNA Methylation Levels}
[phdthesis].
\newblock Mathematisch-Naturwissenschaftlichen Fakultät I der
Humboldt-Universität zu Berlin; 2011.
\newblock Available from:
\url{https://edoc.hu-berlin.de/bitstream/handle/18452/16973/vockentanz.pdf}.
\bibitem{Li1992}
Li E, Bestor TH, Jaenisch R.
\newblock Targeted mutation of the DNA methyltransferase gene results in
embryonic lethality.
\newblock Cell. 1992 Jun;69(6):915--926.
\bibitem{Tucker1996}
Tucker KL, Talbot D, Lee MA, Leonhardt H, Jaenisch R.
\newblock Complementation of methylation deficiency in embryonic stem cells by
a DNA methyltransferase minigene.
\newblock Proc Natl Acad Sci U S A. 1996 Nov;93(23):12920--12925.
\bibitem{Gaudet2003}
Gaudet F, Hodgson JG, Eden A, Jackson-Grusby L, Dausman J, Gray JW, et~al.
\newblock Induction of tumors in mice by genomic hypomethylation.
\newblock Science. 2003 Apr;300(5618):489--492.
\newblock Available from: \url{http://dx.doi.org/10.1126/science.1083558}.
\bibitem{Stresemann2006}
Stresemann C, Brueckner B, Musch T, Stopper H, Lyko F.
\newblock Functional diversity of DNA methyltransferase inhibitors in human
cancer cell lines.
\newblock Cancer research. 2006 Mar;66:2794--2800.
\bibitem{Hollenbach2010}
Hollenbach PW, Nguyen AN, Brady H, Williams M, Ning Y, Richard N, et~al.
\newblock A comparison of azacitidine and decitabine activities in acute
myeloid leukemia cell lines.
\newblock PloS one. 2010 Feb;5:e9001.
\bibitem{Benayoun2014}
Benayoun BA, Pollina EA, Ucar D, Mahmoudi S, Karra K, Wong ED, et~al.
\newblock H3K4me3 breadth is linked to cell identity and transcriptional
consistency.
\newblock Cell. 2014 Jul;158(3):673--688.
\newblock Available from: \url{http://dx.doi.org/10.1016/j.cell.2014.06.027}.
\bibitem{Jeong2014}
Jeong M, Sun D, Luo M, Huang Y, Challen GA, Rodriguez B, et~al.
\newblock Large conserved domains of low DNA methylation maintained by Dnmt3a.
\newblock Nat Genet. 2014 Jan;46(1):17--23.
\newblock Available from: \url{http://dx.doi.org/10.1038/ng.2836}.
\bibitem{Hansen2011}
Hansen KD, Timp W, Bravo HC, Sabunciyan S, Langmead B, McDonald OG, et~al.
\newblock Increased methylation variation in epigenetic domains across cancer
types.
\newblock Nat Genet. 2011 Aug;43(8):768--775.
\newblock Available from: \url{http://dx.doi.org/10.1038/ng.865}.
\bibitem{Berman2012}
Berman BP, Weisenberger DJ, Aman JF, Hinoue T, Ramjan Z, Liu Y, et~al.
\newblock Regions of focal DNA hypermethylation and long-range hypomethylation
in colorectal cancer coincide with nuclear lamina-associated domains.
\newblock Nat Genet. 2012 Jan;44(1):40--46.
\newblock Available from: \url{http://dx.doi.org/10.1038/ng.969}.
\bibitem{Hon2012}
Hon GC, Hawkins RD, Caballero OL, Lo C, Lister R, Pelizzola M, et~al.
\newblock Global DNA hypomethylation coupled to repressive chromatin domain
formation and gene silencing in breast cancer.
\newblock Genome Res. 2012 Feb;22(2):246--258.
\newblock Available from: \url{http://dx.doi.org/10.1101/gr.125872.111}.
\bibitem{Timp2014}
Timp W, Bravo HC, McDonald OG, Goggins M, Umbricht C, Zeiger M, et~al.
\newblock Large hypomethylated blocks as a universal defining epigenetic
alteration in human solid tumors.
\newblock Genome Med. 2014;6(8):61.
\newblock Available from: \url{http://dx.doi.org/10.1186/s13073-014-0061-y}.
\bibitem{Lee2015a}
Lee ST, Muench MO, Fomin ME, Xiao J, Zhou M, {de Smith} A, et~al.
\newblock Epigenetic remodeling in B-cell acute lymphoblastic leukemia occurs
in two tracks and employs embryonic stem cell-like signatures.
\newblock Nucleic Acids Res. 2015 Mar;43(5):2590--2602.
\newblock Available from: \url{http://dx.doi.org/10.1093/nar/gkv103}.
\bibitem{Meuleman2013}
Meuleman W, Peric-Hupkes D, Kind J, Beaudry JB, Pagie L, Kellis M, et~al.
\newblock Constitutive nuclear lamina-genome interactions are highly conserved
and associated with A/T-rich sequence.
\newblock Genome Res. 2013 Feb;23(2):270--280.
\newblock Available from: \url{http://dx.doi.org/10.1101/gr.141028.112}.
\bibitem{Peric-Hupkes2010}
Peric-Hupkes D, Meuleman W, Pagie L, Bruggeman SWM, Solovei I, Brugman W,
et~al.
\newblock Molecular maps of the reorganization of genome-nuclear lamina
interactions during differentiation.
\newblock Mol Cell. 2010 May;38(4):603--613.
\newblock Available from: \url{http://dx.doi.org/10.1016/j.molcel.2010.03.016}.
\bibitem{Issa2004}
Issa JP.
\newblock CpG island methylator phenotype in cancer.
\newblock Nat Rev Cancer. 2004 Dec;4(12):988--993.
\newblock Available from: \url{http://dx.doi.org/10.1038/nrc1507}.
\bibitem{Lee2015}
Lee ST, Wiemels JL.
\newblock Genome-wide CpG island methylation and intergenic demethylation
propensities vary among different tumor sites.
\newblock Nucleic Acids Res. 2015 Oct;Available from:
\url{http://dx.doi.org/10.1093/nar/gkv1038}.
\bibitem{wu2010redefining}
Wu H, Caffo B, Jaffee HA, Irizarry RA, Feinberg AP.
\newblock Redefining CpG islands using hidden Markov models.
\newblock Biostatistics. 2010;p. kxq005.
\newblock Available from: \url{http://rafalab.jhsph.edu/CGI/}.
\bibitem{Hebestreit2013}
Hebestreit K, Dugas M, Klein HU.
\newblock Detection of significantly differentially methylated regions in
targeted bisulfite sequencing data.
\newblock Bioinformatics. 2013 Jul;29(13):1647--1653.
\newblock Available from:
\url{http://dx.doi.org/10.1093/bioinformatics/btt263}.
\bibitem{Ziller2013}
Ziller MJ, Gu H, Müller F, Donaghey J, Tsai LTY, Kohlbacher O, et~al.
\newblock Charting a dynamic DNA methylation landscape of the human genome.
\newblock Nature. 2013 Aug;500(7463):477--481.
\newblock Available from: \url{http://dx.doi.org/10.1038/nature12433}.
\bibitem{Guelen2008}
Guelen L, Pagie L, Brasset E, Meuleman W, Faza MB, Talhout W, et~al.
\newblock Domain organization of human chromosomes revealed by mapping of
nuclear lamina interactions.
\newblock Nature. 2008 Jun;453(7197):948--951.
\newblock Available from: \url{http://dx.doi.org/10.1038/nature06947}.
\bibitem{Stadler2011}
Stadler MB, Murr R, Burger L, Ivanek R, Lienert F, Schöler A, et~al.
\newblock DNA-binding factors shape the mouse methylome at distal regulatory
regions.
\newblock Nature. 2011 Dec;480(7378):490--495.
\newblock Available from: \url{http://dx.doi.org/10.1038/nature10716}.
\bibitem{Schoofs2013}
Schoofs T, Rohde C, Hebestreit K, Klein HU, Göllner S, Schulze I, et~al.
\newblock DNA methylation changes are a late event in acute promyelocytic
leukemia and coincide with loss of transcription factor binding.
\newblock Blood. 2013 Jan;121(1):178--187.
\newblock Available from: \url{http://dx.doi.org/10.1182/blood-2012-08-448860}.
\bibitem{Lister2009}
Lister R, Pelizzola M, Dowen RH, Hawkins RD, Hon G, Tonti-Filippini J, et~al.
\newblock Human DNA methylomes at base resolution show widespread epigenomic
differences.
\newblock Nature. 2009 Nov;462(7271):315--322.
\newblock Available from: \url{http://dx.doi.org/10.1038/nature08514}.
\bibitem{Burger2013}
Burger L, Gaidatzis D, Sch{\"{u}}beler D, Stadler MB.
\newblock Identification of active regulatory regions from DNA methylation
data.
\newblock Nucleic Acids Res. 2013 Sep;41(16):e155.
\newblock Available from: \url{http://dx.doi.org/10.1093/nar/gkt599}.
\bibitem{Kumaraswamy1980}
Kumaraswamy P.
\newblock A generalized probability density function for double-bounded random
processes.
\newblock Journal of Hydrology. 1980;46(1-2):79--88.
\newblock Available from:
\url{http://www.sciencedirect.com/science/article/pii/0022169480900360}.
\bibitem{Jones2009}
Jones M.
\newblock Kumaraswamy’s distribution: A beta-type distribution with some
tractability advantages.
\newblock Statistical Methodology. 2009;6(1):70--81.
\bibitem{Fan2008}
Fan S, Zhang MQ, Zhang X.
\newblock Histone methylation marks play important roles in predicting the
methylation status of CpG islands.
\newblock Biochemical and biophysical research communications.
2008;374(3):559--564.
\bibitem{Zheng2013}
Zheng H, Wu H, Li J, Jiang SW.
\newblock CpGIMethPred: computational model for predicting methylation status
of CpG islands in human genome.
\newblock BMC medical genomics. 2013;6(1):S13.
\bibitem{Hansen2012}
Hansen KD, Langmead B, Irizarry RA.
\newblock BSmooth: from whole genome bisulfite sequencing reads to
differentially methylated regions.
\newblock Genome Biol. 2012 Oct;13(10):R83.
\newblock Available from: \url{http://dx.doi.org/10.1186/gb-2012-13-10-r83}.
\bibitem{Kuan2010}
Kuan PF, Wang S, Zhou X, Chu H.
\newblock A statistical framework for Illumina DNA methylation arrays.
\newblock Bioinformatics. 2010 Nov;26(22):2849--2855.
\newblock Available from:
\url{http://dx.doi.org/10.1093/bioinformatics/btq553}.
\bibitem{Song2013}
Song Q, Decato B, Hong EE, Zhou M, Fang F, Qu J, et~al.
\newblock A reference methylome database and analysis pipeline to facilitate
integrative and comparative epigenomics.
\newblock PLoS One. 2013;8(12):e81148.
\newblock Available from: \url{http://dx.doi.org/10.1371/journal.pone.0081148}.
\bibitem{wood2011fast}
Wood SN.
\newblock Fast stable restricted maximum likelihood and marginal likelihood
estimation of semiparametric generalized linear models.
\newblock Journal of the Royal Statistical Society: Series B (Statistical
Methodology). 2011;73(1):3--36.
\bibitem{rproject}
{R Core Team}. R: A Language and Environment for Statistical Computing.
\newblock Vienna, Austria; 2015.
\newblock Available from: \url{http://www.R-project.org/}.
\bibitem{Wood2003}
Wood SN.
\newblock {Thin-plate regression splines}.
\newblock {Journal of the Royal Statistical Society: Series B (Statistical
Methodology)}. 2003;65(1):95--114.
\bibitem{Iurlaro2017}
Iurlaro M, von Meyenn F, Reik W.
\newblock DNA methylation homeostasis in human and mouse development.
\newblock Current opinion in genetics \& development. 2017 Apr;43:101--109.
\bibitem{Cruickshanks2013}
Cruickshanks HA, McBryan T, Nelson DM, Vanderkraats ND, Shah PP, {van Tuyn} J,
et~al.
\newblock Senescent cells harbour features of the cancer epigenome.
\newblock Nat Cell Biol. 2013 Dec;15(12):1495--1506.
\newblock Available from: \url{http://dx.doi.org/10.1038/ncb2879}.
\bibitem{Crane2015}
Crane E, Bian Q, McCord RP, Lajoie BR, Wheeler BS, Ralston EJ, et~al.
\newblock Condensin-driven remodelling of X chromosome topology during dosage
compensation.
\newblock Nature. 2015 Jul;523:240--244.
\bibitem{Wilson2016}
Wilson NK, Schoenfelder S, Hannah R, {S{\'{a}}nchez Castillo} M, Sch{\"{u}}tte
J, Ladopoulos V, et~al.
\newblock Integrated genome-scale analysis of the transcriptional regulatory
landscape in a blood stem/progenitor cell model.