Todd Scott Macfarlan, Ph.D.

Stadtman Investigator

Unit on Mammalian Epigenome Reprogramming


6B 2B211


Research Topics

Evolving Mechanisms of Transcriptional Control in Mammals

Exploring the regulation and function of endogenous retroviruses

Endogenous retroviruses (ERVs) are the remnants of ancient retroviral infections that have become a permanent part of the host genome. These sequences make up nearly 10% of mammalian genomes. It has long been debated whether ERVs and other transposable elements are nothing more than parasitic elements that have remained in genomes due to their ability to independently replicate (via retrotransposition) or whether they may provide some selective advantage to their hosts. One way in which ERVs can influence their hosts is via regulation of host gene expression. ERVs and other transposons are targeted for silencing by distinct repressive chromatin generating machinery that can spread to neighboring genes, or can serve as alternate promoters. We have been studying a particular class of ERVs found in all placental mammals called ERVLs (MERVLs in the mouse) that very briefly evade silencing in preimplantation development during zygote genome activation. Morever these ERVL elements appear to serve as primary or alternate promoters for a large number cellular genes, which has lead us to speculate that these elements may actually be essential for embryo development. We are interested in two important questions, 1) How are ERVL elements regulated? and 2) Are ERVL elements critical for cell fate decisions in embryo development?

Exploring the  function of the rapidly evolving KRAB-ZFP gene family

Kruppel associated box zinc finger proteins (KRAB-ZFPs) have emerged as candidates that recognize ERVs.   KRAB-ZFPs are rapidly evolving transcriptional repressors that emerged in tetrapods.  They make up the largest family of transcription factors in mammals (estimated to be ~200-300 in mice and humans).  Each species has its own unique repertoire of KRAB-ZFPs, with a small number shared with closely related species and a larger fraction specific to each species.  Despite their abundance, little is known about their physiological functions. KRAB-ZFPs consist of an N-terminal KRAB domain that binds the co-repressor KAP1and a variable number of C-terminal C2H2 zinc finger domains that mediate sequence-specific DNA binding. KAP1 directly interacts with the KRAB domain, which recruits the histone methyltransferase (HMT) SETDB1 and heterochromatin protein 1 (HP1) to initiate heterochromatic silencing. Several lines of evidence point to a role for the KRAB-ZFP family in ERV silencing. First, the number of C2H2 zinc finger genes in mammals correlates with the number of ERVs.  Second, the KRAB-ZFP protein ZFP809 was isolated based on its ability to bind to the primer binding site for proline tRNA (PBSPro) of murine leukemia virus (MuLV). Third, deletion of the KRAB-ZFP co-repressors Trim28 or Setdb1 leads to activation of many ERVs.  Thus we have begun a systematic interrogation of KRAB-ZFP function as a potential adaptive repression system against ERVs.  Our ongoing studies have lead us to speculate that the arms race between ERVs and KRAB-ZFPs has played an important role not only in the evolution of gene regulatory networks in mammals but in speciation itself.

Exploring the function of histone modifying enzymes during development

A large number of enzymes that post-translationally modify histones/DNA have been identified and biochemically characterized. A number of these enzymes have also been shown to be essential for embryo development, mutated in cancers and neurological disease, or important for transgenerational epigenetic inheritance in model organisms. We are using stem cell based models of development along with mouse genetics to remove enzymes that post translationally modify histones and DNA in a tissue specific manner. In particular we are focusing on the time period of preimplantation development, where massive reprogramming of the epigenome takes place, and during formation of the central nervous system, when cells are becoming post-mitotic as they differentiate into neurons and are thus incapable of replication dependent changes in the epigenome. With these studies, we hope to gain a further understanding of the importance of epigenetic information stored in chromatin.

Studying the interplay of transcription factors and chromatin modifying enzymes

Transcription factors have long been known to be the master regulators of cell fate, binding to specific sequences of DNA and activating or silencing genes that allow specific cell types to carry out specialized function. More recently, it has been demonstrated that transcription factors can convert somatic cells into induced pluripotent cells (iPS cells) or from one somatic type to another, although this process is relatively inefficient. One likely reason this process is so inefficient is that differentiated cell types carry “restrictive” epigenomes that are less accessible to transcription factors than the “permissive” epigenomes of embryonic stem cells, which are easily reprogrammed to somatic cells. We are thus exploring the possibility that chromatin-modifying enzymes gate the activity of transcription factors during these reprogramming processes (both natural and artificial reprogramming), and are testing how chromatin-modifying enzymes work in conjuction with transcription factors to regulate cell fate.


Dr. Todd Macfarlan earned his Ph.D. in Cell and Molecular Biology from the University of Pennsylvania in 2000, where his interest in epigenetic phenomena began while studying the histone binding and transcriptional repressive activities of THAP domain proteins. After his Ph.D., Dr. Macfarlan joined the laboratory of Dr. Samuel Pfaff at the Salk Institute for Biological Studies, where he continued to study chromatin and epigenome changes during mammalian embryo development. He was then recruited to the NIH in July of 2012 as part of the Earl Stadtman Investigator search, in chromosome biology and epigenetics. As a member of the Program in Genomics of Differentiation, NICHD, Dr. Macfarlan heads the Unit on Mammalian Epigenome Reprogramming.

Selected Publications

  1. Patel A, Yang P, Tinkham M, Pradhan 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;173(1):221-233.e12.

  2. Yang P, Wang Y, Hoang D, Tinkham M, Patel A, Sun MA, Wolf G, Baker M, Chien HC, Lai KN, Cheng X, Shen CJ, Macfarlan TS. A placental growth factor is silenced in mouse embryos by the zinc finger protein ZFP568. Science. 2017;356(6339):757-759.

  3. 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;548(7665):E1-E3.

  4. Wolf G, Yang P, Füchtbauer AC, Füchtbauer EM, Silva AM, Park C, Wu W, Nielsen AL, Pedersen FS, Macfarlan TS. The KRAB zinc finger protein ZFP809 is required to initiate epigenetic silencing of endogenous retroviruses. Genes Dev. 2015;29(5):538-54.

  5. Macfarlan TS, Gifford WD, Driscoll S, Lettieri K, Rowe HM, Bonanomi D, Firth A, Singer O, Trono D, Pfaff SL. Embryonic stem cell potency fluctuates with endogenous retrovirus activity. Nature. 2012;487(7405):57-63.

This page was last updated on September 4th, 2018