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Convergent evolution New paper from the lab is now online in PNAS. This project was led by our collaborator Lynne Maquat from University of Rochester Medical Center. In the paper, we suggest that independently evolved SINEs have accumulated in the 3'UTRs of orthologous human and mouse genes. We demonstrate that, in some cases, this has resulted in their regulating gene expression by Staufen-mediated mRNA decay (SMD) in human and mouse myoblasts. Thus, SINE-directed SMD has convergently evolved to regulate myoblast metabolism. This represents an example of the convergent evolution of posttranscriptional gene regulation using SINEs.

Bronwyn A. Lucas, Eitan Lavi, Lily Shiue, Hana Cho, Sol Katzman, Keita Miyoshi, Mikiko C. Siomi, Liran Carmel, Manuel Ares, Jr., and Lynne E. Maquat (2018). Evidence for convergent evolution of SINE-directed Staufen-mediated mRNA decay, PNAS early edition.

graduationCongratulations to David Gokhman, whose PhD had been approved. From now on, it's Dr Gokhman for you.

Gene ORGANizer Gene ORGANizer, our web server connecting genes to the body parts they affect, is among the top research tools of 2017.

graduationCongratulations to Fouad Zahdeh, whose PhD had been approved today. Good job Dr Zahdeh.

conferenceA very successful conference, Human Evolution: Fossils, Ancient and Modern Genomes, just ended at the Wellcome Genome Campus in Hinxton, Cambridge, UK. From the lab, we were represented by Liran Carmel and David Gokhman. Liran gave a talk on DNA methylation-based reconstruction of the Denisovan anatomy, and Shai Carmi gave a talk on our work on Bronze and Iron Age populations in Israel.

Enviornmental paleoepigenetics New paper from the lab is now published in Molecular Biology & Evolution. This paper suggests a forward-looking research direction, to which we call environmental paleoepigenetics. The idea is to use known response patterns of DNA methylation to changes in environmental conditions in order to reconstruct the environments in which ancient individuals lived. We review what is known today about such response patterns, and demonstrate the applicability of our approach by showing that DNA methylation of ancient hunter-gatherers are compatible with hungery seasons in current African populations.

David Gokhman, Anat Malul, Liran Carmel (2017). Inferring past environments from ancient epigenomes, Molecular Biology & Evolution 34:2429-2438.

Research Interests:
Our lab deals with a host of topics in the general fields of molecular evolution and genetics. Among the topics that are currently pursued are:
  • Human evolution. Recent advances in ancient DNA sequencing yielded genomes (either shotgun sequences with varying degrees of coverage, or SNP arrays) of many ancient anatomically modern humans, as well as of Neanderthals and Denisovans. This open unique opportunities to study the genetic aspects of the very recent lag of our own evolution.
  • Paleo-epigenetics. We developed a technique to reconstruct full DNA methylation maps from high-coverage ancient genomes, and use it to study evolutionary changes in gene regulation, ancient environments and phenotypic adaptations.
  • Paleo-genetics. We study the genetic structure of ancient populations in Israel.
  • RNA biology. We are studying many aspects of RNA biology, including splicing, nonsense-mediated decay, 3'-end processing, and circular RNAs.
  • Multivariate data analysis. My lab is also active in some fields of applied mathematics: multivariate analysis, statistical pattern recognition, data visualization, and machine learning.
A quick summary of our research on archaic gene regulation. A narration accompanied by whiteboard animation.

Interview Yoav Mathov was interviewed in Makademia.

MovieLiran was interviewed at London et Kirshenbaum about Otzi's helicobacter. Minutes 29:42 to 34:33.

Our Web Servers
Movie Gene ORGANizer connects genes to the body parts where their phenotype is observed. Given a list of genes, Gene ORGANizer finds body parts in which these genes are enriched or depleted. The paper is about to appear in the webserver issue of NAR, but can already be found online.

Movie JuncDB is a gene exon-intron architecture comparative database, covering nearly 40,000 sets of orthologous transcripts across 88 eukaryotic species. It had been published in the database issue of NAR.
Contact Information:
Room 2-342
Department of Genetics, The Alexander Silberman Institute of Life Sciences, Faculty of Science,
the Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 91904, Israel
telephone +972 (2) 658-5103
fax +972 (2) 658-4856
email liran.carmel @
The Hebrew University
Useful links: for more details and full list