Publications

Primary Research Publications

  • Hoge C, de Manuel M, Mahgoub M, Okami N, Fuller Z, Banerjee S, Baker Z, McNulty M, Andolfatto P, Macfarlan TS, Schumer M, Tzika AC, Przeworski M. Patterns of recombination in snakes reveal a tug-of-war between PRDM9 and promoter-like features. Science. 2024 Feb 23;383(6685):eadj7026. doi: 10.1126/science.adj7026. Epub 2024 Feb 23.PMID: 38386752
  • Sala L, Kumar M, Prajapat M, Chandrasekhar S, Cosby RL, La Rocca G, Macfarlan TS, Awasthi P, Chari R, Kruhlak M, Vidigal JA. AGO2 silences mobile transposons in the nucleus of quiescent cells. Nat Struct Mol Biol. 2023 Dec;30(12):1985-1995. doi: 10.1038/s41594-023-01151-z. Epub 2023 Nov 20.PMID: 37985687
  • Xie G, Lee JE, Senft AD, Park YK, Jang Y, Chakraborty S, Thompson JJ, McKernan K, Liu C, Macfarlan TS, Rocha PP, Peng W, Ge K. MLL3/MLL4 methyltransferase activities control early embryonic development and embryonic stem cell differentiation in a lineage-selective manner. Nat Genet. 2023 Apr;55(4):693-705. doi: 10.1038/s41588-023-01356-4. Epub 2023 Apr 3.PMID: 37012455
  • Du C, Jiang J, Li Y, Yu M, Jin J, Chen S, Fan H, Macfarlan TS, Cao B, Sun MA. Regulation of endogenous retrovirus-derived regulatory elements by GATA2/3 and MSX2 in human trophoblast stem cells. Genome Res. 2023 Feb;33(2):197-207. doi: 10.1101/gr.277150.122. Epub 2023 Feb 17.PMID: 36806146
  • Sun MA, Wolf G, Wang Y, Senft AD, Ralls S, Jin J, Dunn-Fletcher CE, Muglia LJ, Macfarlan TS. Endogenous Retroviruses drive lineage-specific regulatory evolution across primate and rodent placentae. Mol Biol Evol. 2021 Jul 28:msab223. doi: 10.1093/molbev/msab223.PMID: 34320657
  • Agarwal S, Bonefas KM, Garay PM, Brookes E, Murata-Nakamura Y, Porter RS, Macfarlan TS, Ren B, Iwase S. KDM1A maintains genome-wide homeostasis of transcriptional enhancers. Genome Res. 2021 Jan 7;31(2):186-97. doi: 10.1101/gr.234559.118
  • Bertozzi TM, Elmer JL, Macfarlan TS, Ferguson-Smith AC. KRAB zinc finger protein diversification drives mammalian interindividual methylation variability. PNAS. 2020 Dec 8;117(49):31290-31300. Doi: 10.1073/pnas.2017053117 PMID:33239447
  • Kumar J, Kaur G, Ren R, Lu Y, Lin K, Li J, Huang Y, Patel A, Barton MC, Macfarlan T, Zhang X, Cheng X.  KRAB domain of ZFP568 disrupts TRIM28-mediated abnormal interactions in cancer cells. NAR Cancer. 2020 Jun;2(2):zcaa007. doi: 10.1093/narcan/zcaa007. Epub 2020 May 18. PMID: 32743551
  • Wolf G, de Iaco A, Sun MA, Bruno M, Tinkham M, Hoang D, Mitra A, Ralls S, Trono D, Macfarlan TS*.  KRAB-zinc finger protein gene expansion in response to active retrotransposons in the murine lineage. Elife. 2020 Jun 1;9:e56337. doi: 10.7554/eLife.56337.PMID: 32479262
  • Mahgoub M, Paiano J, Bruno M, Wu W, Pathuri S, Zhang X, Ralls S, Cheng X, Nussenzweig A, Macfarlan TS*. Dual histone methyl reader ZCWPW1 facilitates repair of meiotic double strand breaks in male mice.  Elife. 2020 Apr 30;9:e53360. doi: 10.7554/eLife.53360.PMID: 32352380
  • Chen C, Sun MA, Warzecha C, Bachu M, Dey A, Wu T, Adams PD, Macfarlan T, Love P, Ozato K. HIRA, a DiGeorge Syndrome Candidate Gene, Confers Proper Chromatin Accessibility on HSCs and Supports All Stages of Hematopoiesis.  Cell Rep. 2020 Feb 18;30(7):2136-2149.e4. doi: 10.1016/j.celrep.2020.01.062.PMID: 32075733
  • Yang F, Huang X, Zang R, Chen J, Fidalgo M, Sanchez-Priego C, Yang J, Caichen A, Ma F, Macfarlan T, Wang H, Gao S, Zhou H, Wang J. DUX-miR-344-ZMYM2-Mediated Activation of MERVL LTRs Induces a Totipotent 2C-like State. Cell Stem Cell. 2020 Feb 6;26(2):234-250.e7. doi: 10.1016/j.stem.2020.01.004.PMID: 32032525
  • Seah MKY, Wang Y, Goy PA, Loh HM, Peh WJ, Low DHP, Han BY, Wong E, Leong EL, Wolf G, Mzoughi S, Wollmann H, Macfarlan TS, Guccione E, Messerschmidt DM. The KRAB-zinc finger protein ZFP708 mediates epigenetic repression at RMER19B retrotransposons. Development. 2019 Apr 1. pii: dev.170266. doi: 10.1242/dev.170266. PMID:30846446
  • Dunn-Fletcher CE, Muglia LM, Pavlicev M, Wolf G, Sun MA, Hu YC, Huffman E, Tumukuntala S, Thiele K, Mukherjee A, Zoubovsky S, Zhang X, Swaggart KA, Lamm KYB, Jones H, Macfarlan TS, Muglia LJ.  Anthropoid primate-specific retroviral element THE1B controls expression of CRH in placenta and alters gestation length. PLoS Biol. 2018 Sep 19;16(9):e2006337. doi: 10.1371/journal.pbio.2006337. PMID:30231016
  • Patel A1, Yang P1, Tinkham M, Pradham M, Sun MA, Wang Y, Hoang D, Wolf G, Horton JR, Zhang X, Macfarlan T*, Cheng X*. DNA conformation induces adaptable binding by tandem zinc finger proteins. Cell 2018. Mar 22;173(1):221-233.e12  doi.org/10.1016/j.cell.2018.02.0581. PMID:29551271
  • Wolf G, Rebollo R, Karimi MM, Ewing AD, Kamada R, Wu W, Wu B, Bachu M, Ozato K, Faulkner GJ, Mager DL, Lorincz MC, Macfarlan TS*. On the role of H3.3 in retroviral silencing.  Nature 2017 Aug 3; 548E1-E3. doi:10.1038/nature23277. PMID:28770848
  • Yang P, Wang Y, Hoang D, Tinkham M, Patel A, Sun M-A, Wolf G, Baker M, Chien H-C, Lai N, Cheng X, Shen C-K J, and Macfarlan TS*. A placental growth factor is silenced in mouse embryos by the zinc finger protein ZFP568.  Science 2017 May 19;356(6339):757-759. doi: 10.1126/science.aah6895.  PMID:28522536
  • Choi YJ, Lin CP, Risso D, Chen S, Kim TA, Tan MH, Li JB, Wu Y, Chen C, Xuan Z, Macfarlan T, Peng W, Lloyd K, Kim SY, Speed TP, He L.  Deficiency of microRNA miR-34a expands cell fate potential in pluripotent stem cells.  Science 2017 Jan 12. pii: aag1927. doi: 10.1126/science.aag1927. PMID:28082412
  • Wang C, Lee J-E, Lai B, Macfarlan TS Xu B, Zhuang L, Liu C, Peng W, Ge K.  Enhancer priming by H3K4 methyltransferase MLL4 controls cell fate transition. Proc Natl Acad Sci U S A. 2016 Oct 3. pii: 201606857.
  • Wasson JA, Simon AK, Myrick DA, Wolf G, Driscoll S, Pfaff SL, Macfarlan TS*, and Katz DJ*.  Maternally provided LSD1/KDM1A enables the maternal-to-zygotic transition and prevents defects that manifest postnatally.  Elife 2016, 10.7554/eLife.08848.  DOI: http://dx.doi.org/10.7554/eLife.08848. external link PMID:26814574
  • Geeven G, Zhu Y, Kim BJ, Bartholdy BA, Yang SM, Macfarlan TS, Gifford WD, Pfaff SL, Verstegen MJ, Pinto H, Vermunt MW, Creyghton MP, Wijchers PJ, Stamatoyannopoulos JA, Skoultchi AI, de Laat W.  Local compartment changes and regulatory landscape alterations in histone H1-depleted cells.  Genome Biol. 2015 Dec 23; 16(1):289.  Doi: 10.1186/s13059-015-0857-0. PMID:26700097
  • Wang J, Telese F, Tan Y, Li W, Jin C, He X, Basnet H, Ma Q, Merkurjev D, Zhu X, Liu Z, Zhang J, Ohgi K, Taylor H, White RR, Macfarlan TS, Pfaff SL, Rosenfeld MG.  LSD1n is a H4K20 demethylase regulating memory formation via transcriptional elongation control.  Nature Neurosci. 2015 Jul 27. doi: 10.1038/nn.4069.  PMID:26214369
  • Lee H, Kim M, Kim N, Macfarlan T, Pfaff SL, Mastick GS, Song MR. Slit and Semaphorin signaling governed by Islet transcription factors positions motor neuron somata within the neural tube. Exp Neurol. 2015 Apr 3. pii: S0014-4886(15)00100-4. doi: 10.1016/j.expneurol.2015.03.024. PMID:25843547
  • Wolf G, Yang P, Fuchtbauer A, Fuchtbauer EM, Silva AM, Park C, Nielsen AL, Pedersen FS, and Macfarlan TS*.  The KRAB zinc finger protein ZFP809 is required to initiate epigenetic silencing of endogenous retroviruses. Genes Dev. 2015 Mar1; 29(5):538-54.  doi: 10.1101/gad.252767.114. PMID:25737282
  • Agarwal S, Macfarlan TS, and Iwase S. Sequencing of First-strand cDNA library reveals full-length transcriptomes., Nature Communications. 2015 Jan 21; 6:6002 doi: 10.1038/ncomms7002. PMID:25607527
  • Rowe HM, Kapopoulou A, Corsinotti A, Fasching L, Macfarlan TS, Tarabay Y, Viville S, Jakobsson J, Pfaff SL, Trono D.  TRIM28 repression of retrotransposon-based enhancers is necessary to preserve transcriptional dynamics in embryonic stem cells. Genome Res. 2013 Mar;23(3):452-61. doi: 10.1101/gr.147678.112. PMID:23233547
  • Macfarlan TS, Gifford WD, Driscoll S, Rowe HM, Bonanomi D, Lettieri K, Firth A, Singer O, Trono D, and Pfaff SL.  Embryonic stem cell potency fluctuates with endogenous retrovirus activity. Nature. 2012 Jun 13 doi: 10.1038/nature11244.  PMID:22722858
  • Macfarlan TS, Gifford WD, Agarwal SA, Driscoll S, Lettieri K, Wang J, Andrews SE, Franco L, Rosenfeld MG, Ren B, and Pfaff SL. Endogenous retroviruses and neighboring genes are coordinately repressed by LSD1/KDM1A. Genes Dev. 2011 Mar 15;25(6):594-607.  PMID: 21357675

Reviews/Previews

  • Senft AD, Macfarlan TS. Transposable elements shape the evolution of mammalian development. Nat Rev Genet. 2021 Nov;22(11):691-711. doi: 10.1038/s41576-021-00385-1. Epub 2021 Aug 5.PMID: 34354263
  • Haase AD and Macfarlan TS. PiRNAs Rise to Rescue Koalas.  Cell. 2019 Oct 17;179(3):582-583. doi: 10.1016/j.cell.2019.09.025. PMID: 31626765.
  • Bruno M, Mahgoub M, and Macfarlan TS. The arms race between KRAB-Zinc Finger Proteins and Endogenous Retroelements and its impact on mammals.  Annu Rev Genet. 2019 Sep 13. Doi: 10.1146/annurev-genet-112618-043717. PMID 31518518
  • Honson DD, Macfarlan TS. A lncRNA-like Role for LINEs in Develoment. Dev Cell. 2018 Jul 16;46(2):132-134. doi: 10.1016/j.devcel.2018.06.022. PMID: 30016617
  • Yang P, Wang Y, Macfarlan TS*.  The Role of KRAB-ZFPs in Transposable Element Repression and Mammalian Evolution. Trends Genet. 2017 Sep 18. pii: S0168-9525(17)30144-0. doi: 10.1016/j.tig.2017.08.006. PMID:28935117
  • Thompson PJ, Macfarlan TS*, and Lorincz MC*.  Long terminal repeats: from parasitic elements to building blocks of the transcriptional regulatory repertoire. Mol Cell. 2016 June 2, 62(5):766-76. Doi: 10.1016/j.molcell.2016.03.029. PMID:27259207
  • Wolf G, Greenberg D, Macfarlan TS*.  Spotting the enemy within: Targeted silencing of foreign DNA in mammalian genomes by the Kruppel-associated box zinc finger protein family. Mobile DNA. 2015, 6:17. Doi:10.1186/s13100-015-0050-8. PMID:26435754
  • Wolf G, Macfarlan TS*.  Revealing the complexity of retroviral repression. Cell. 2015 Sep 24; 163 (1):30-2. Doi:10.1016/j.cell.2015.09.014. PMID:26406368
  • Yang P, Wu W, and Macfarlan TS*. A combination of maternal histone variants and chaperones promotes paternal genome activation and boosts somatic cell reprogramming. Bioessays, 2014 Oct 18, doi110.1002/bies.201400072. PMID:25328107
  • Gifford WD, Pfaff SL, and Macfarlan TS*, Transposable elements as genetic regulatory substrates in early development.  Trends Cell Biol. 2013 May; 23 (5): 218-26. doi 10.1016/j.tcb.2013.01.001. PMID:23411159

1 Indicates co-first authors  *indicates co-corresponding authors

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