Lily Agranat-Tamir's research while affiliated with Hebrew University of Jerusalem and other places

Publications (10)

Article
Motivation: The rise in the number of genotyped ancient individuals provides an opportunity to estimate population admixture models for many populations. However, in models describing modern populations as mixtures of ancient ones, it is typically difficult to estimate the model mixing coefficients and to evaluate its fit to the data. Results: W...
Article
We report genome-wide DNA data for 73 individuals from five archaeological sites across the Bronze and Iron Ages Southern Levant. These individuals, who share the “Canaanite” material culture, can be modeled as descending from two sources: (1) earlier local Neolithic populations and (2) populations related to the Chalcolithic Zagros or the Bronze A...
Article
Full-text available
Changes in potential regulatory elements are thought to be key drivers of phenotypic divergence. However, identifying changes to regulatory elements that underlie human-specific traits has proven very challenging. Here, we use 63 reconstructed and experimentally measured DNA methylation maps of ancient and present-day humans, as well as of six chim...
Preprint
Full-text available
Regulatory changes are broadly accepted as key drivers of phenotypic divergence. However, identifying regulatory changes that underlie human-specific traits has proven very challenging. Here, we use 63 DNA methylation maps of ancient and present-day humans, as well as of six chimpanzees, to detect differentially methylated regions that emerged in m...
Article
A-to-I RNA editing is a conserved widespread phenomenon in which adenosine (A) is converted to inosine (I) by adenosine deaminases (ADARs) in double-stranded RNA regions. Although human RNAs contain millions of A-to-I editing sites, most of these occur in noncoding regions and their function is unknown. Mutations in ADAR enzymes in C. elegans cause...
Article
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C/D box small nucleolar RNAs (SNORDs) are small noncoding RNAs, and their best-understood function is to target the methyltransferase fibrillarin to rRNA (for example, SNORD27 performs 2'-O-methylation of A27 in 18S rRNA). Unexpectedly, we found a subset of SNORDs, including SNORD27, in soluble nuclear extract made under native conditions, where fi...
Article
Full-text available
MicroRNAs (miRNAs) are central regulators of gene expression, and a large fraction of them are encoded in introns of RNA polymerase II transcripts. Thus, the biogenesis of intronic miRNAs by the microprocessor and the splicing of their host introns by the spliceosome require coordination between these processing events. This cross-talk is addressed...
Article
Full-text available
The serotonin receptor 2C (HTR2C) gene encodes a G protein-coupled receptor that is exclusively expressed in neurons. Here, we report that the 5′ untranslated region of the receptor pre-mRNA as well as its hosted miRNAs is widely expressed in non-neuronal cell lines. Alternative splicing of HTR2C is regulated by MBII-52. MBII-52 and the neighboring...

Citations

... These methylation differences were enriched within a network of genes (e.g., NFIX and SOX9) involved in the spatiotemporal patterning of skeletal development and growth, particularly in genes affecting the protrusion of the lower midface and size of the nose. 131 In modern humans, the NFIX gene locus is hypermethylated compared to that for archaic hominins. 131 Across modern human and mouse tissues, increased NFIX methylation is correlated with decreased NFIX expression, and NFIX knock-out mice have vocal tract anatomy alterations that mirror the general configuration of modern humans, with a more caudal positioning of the tongue and descent of the hyoid-larynx lower into the throat-positioning that for modern humans is critical to speech production. ...
... These include descriptions of the earliest local farming groups from the Neolithic 1 and their expansions into Europe 2,3 as well as genetic differentiation among contemporary Neolithic groups [4][5][6] . In the later Chalcolithic period, evidence of distinctive cultural practices and associated population movements highlight the dynamic history of the region, especially in the Southern Levant 7,8 . Further, genomic studies from the Bronze to Iron Ages in the Levant also report admixture and population movements, suggesting some degree of continuity with modern populations 6,[9][10][11] . ...
... While the important role genetic regulation in human evolution has been highlighted by previous studies [18][19][20][21], we find that species-specific variants above a high frequency threshold have a previously underexplored role in human brain evolution. We show that regions under putative positive selection are enriched in derived, high-frequency (HF) eQTLs, and that the pituitary and cerebellum have a significantly higher number of regulatory variability compared to other tissues and a control set. ...
... Next, variant quality filtering was applied, which included removing heterozygous variants; removing sites in dbSNP (version 150); removing intronic sites within 4bp of splice junctions; and removing sites within homopolymers ≥ 5bp. After that, the reads were checked with BLAT [25] and A-to-G transitions were taken as potential A-to-I RESs [16,[26][27][28][29]. In total, 171,909 A-to-I RESs were identified, and thirty-five regions that harboured 80 RESs were randomly selected for validation by Sanger sequencing. ...
... Thus it is tempting to speculate that they may serve to guide modifications of other classes of RNA, such as mRNA. Indeed, there is considerable evidence for interactions forming between snoRNAs and mRNAs (25)(26)(27)(28)(29) in addition to limited evidence also for snoRNA-directed modifications on mRNA (14,30). Second, if snoRNA-guided pseudouridylation of mRNA can occur, then understanding the rules guiding such activity can be exploited therapeutically. ...
... hnRNPC and U2AF2 compete for common binding sites, specifically single-stranded structures within polypyrimidine tracts 51,52 , and regulate pre-mRNA splicing by associating with the spliceosome 53 . In addition, Agranat-Tamir et al. reported that spliceosomes can interact with microprocessors 54 . These studies support the possibility of direct competition between hnRNPC and U2AF2 to regulate isomiR-21-5p | ±1 biogenesis. ...
... In fact, 5-HT 2C receptor is encoded by a complex transcription unit, which includes the coding region and an extended 5′ untranslated region containing two introns and three exons, which host miRNAs. These miRNAs can bind to mRNA, and therefore, block translation, causing RNA decay or cleavage, or chromatin silencing [53]. On the other hand, Tang et al. [54] found that the levels of histone acetylation associated with Htr2c promoter are correlated with its gene expression levels. ...