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Research: Molecular and genetic landscapes of retina and brain microglia in neurodegenerative diseases
- Khang Ma and
- Rinki Ratnapriya
Genome Res. October 2025 35: 2143-2157; Published in Advance August 26, 2025, doi:10.1101/gr.280554.125
...than 1.5 in retina or brain microglia. Among these, several AMD-associated genes showed selective or preferential expression in retina microglia (Fig. 5E), whereas those linked to AD exhibited similar patterns in brain microglia (Fig. 5H; Hansen et al. 2018). We observed that AMD genes that were highly...
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Research: The evolution of duplicate gene expression in mammalian organs
- Katerina Guschanski,
- Maria Warnefors,
- and Henrik Kaessmann
Genome Res. September 2017 27: 1461-1474; Published in Advance July 25, 2017, doi:10.1101/gr.215566.116
...-specific duplications in primates and marsupials. Expansions along the primate lineage produced paralogs with high brain-specific expression, whereas the majority of opossum genes show low liver-specific expression. Guschanski et al. 1470 Genome Research www..org be important to systematically study transcriptional...
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Research: Conserved microRNA targeting reveals preexisting gene dosage sensitivities that shaped amniote sex chromosome evolution
- Sahin Naqvi,
- Daniel W. Bellott,
- Kathy S. Lin,
- and David C. Page
Genome Res. April 2018 28: 474-483; Published in Advance February 15, 2018, doi:10.1101/gr.230433.117
...that distinguish classes of X- and Z-linked genes is thus crucial to understanding the selective pressures underlying the molecular events of mammalian and avian sex chromosome evolution.Emerging evidence suggests a role for gene dosage sensitivity in mammalian and avian sex chromosome evolution. X- and Z...
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Research: Alternative splicing modulated by genetic variants demonstrates accelerated evolution regulated by highly conserved proteins
- Yun-Hua Esther Hsiao,
- Jae Hoon Bahn,
- Xianzhi Lin,
- Tak-Ming Chan,
- Rena Wang,
- and Xinshu Xiao
Genome Res. April 2016 26: 440-450; Published in Advance February 17, 2016, doi:10.1101/gr.193359.115
...-nucleotide variants (SNVs) all demonstrated positive selection or accelerated evolution in primates. We predicted that GMAS SNVs often alter binding of splicing factors, with SRSF1 affecting the most GMAS events and demonstrating global allelic binding bias. However, in contrast to their GMAS targets, the predicted...
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Resource: Annotation and cluster analysis of spatiotemporal- and sex-related lncRNA expression in rhesus macaque brain
- Siling Liu,
- Zhengbo Wang,
- Dong Chen,
- Bowen Zhang,
- Ren-Rong Tian,
- Jing Wu,
- Ying Zhang,
- Kaiyu Xu,
- Liu-Meng Yang,
- Chao Cheng,
- Jian Ma,
- Longbao Lv,
- Yong-Tang Zheng,
- Xintian Hu,
- Yi Zhang,
- Xiangting Wang,
- and Jiali Li
Genome Res. September 2017 27: 1608-1620; Published in Advance July 7, 2017, doi:10.1101/gr.217463.116
...contributor to brain architecture and functional evolution, as well as to the development process and aging (Belgard et al. 2011; Aprea et al. 2013; Telley et al. 2016). Long noncoding RNAs (lncRNAs) are a subgroup of RNA longer than 200 nucleotides (nt), yet have limited protein-coding potential. Many lnc...
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Resource: Single-cell-resolution transcriptome map of human, chimpanzee, bonobo, and macaque brains
- Ekaterina Khrameeva,
- Ilia Kurochkin,
- Dingding Han,
- Patricia Guijarro,
- Sabina Kanton,
- Malgorzata Santel,
- Zhengzong Qian,
- Shen Rong,
- Pavel Mazin,
- Marat Sabirov,
- Matvei Bulat,
- Olga Efimova,
- Anna Tkachev,
- Song Guo,
- Chet C. Sherwood,
- J. Gray Camp,
- Svante Pääbo,
- Barbara Treutlein,
- and Philipp Khaitovich
Genome Res. May 2020 30: 776-789; Published in Advance May 18, 2020, doi:10.1101/gr.256958.119
...reconstructed for each brain region are shown in Supplemental Figure S5. (J) Total branch length calculated for the reconstructed phylogenetic trees for each of the 33 brain regions grouped by expression-based regional clusters I–VII, defined in G.Of the 11,176 detected orthologous protein-coding genes, 2801...
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Resource: A comparison of gene expression and DNA methylation patterns across tissues and species
- Lauren E. Blake,
- Julien Roux,
- Irene Hernando-Herraez,
- Nicholas E. Banovich,
- Raquel Garcia Perez,
- Chiaowen Joyce Hsiao,
- Ittai Eres,
- Claudia Cuevas,
- Tomas Marques-Bonet,
- and Yoav Gilad
Genome Res. February 2020 30: 250-262; Published in Advance January 17, 2020, doi:10.1101/gr.254904.119
...patterns are consistent with the action of natural selection. Together, these observations consistently support the inference that when genes perform an important function that needs to be carefully regulated, evolution can act on multiple levels of the regulatory cascade in primates.Focusing on species...
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Research: Comprehensive identification and analysis of human accelerated regulatory DNA
- Rachel M. Gittelman,
- Enna Hun,
- Ferhat Ay,
- Jennifer Madeoy,
- Len Pennacchio,
- William S. Noble,
- R. David Hawkins,
- and Joshua M. Akey
Genome Res. September 2015 25: 1245-1255; Published in Advance June 23, 2015, doi:10.1101/gr.192591.115
..., Berkeley, California 94701, USA Corresponding author: akeyj@uw.edu Abstract It has long been hypothesized that changes in gene regulation have played an important role in human evolution, but regulatory DNA has been much more difficult to study compared with protein-coding regions...
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Resource: The landscape of miRNA editing in animals and its impact on miRNA biogenesis and targeting
- Lishi Li,
- Yulong Song,
- Xinrui Shi,
- Jianheng Liu,
- Shaolei Xiong,
- Wanying Chen,
- Qiang Fu,
- Zichao Huang,
- Nannan Gu,
- and Rui Zhang
Genome Res. January 2018 28: 132-143; Published in Advance December 12, 2017, doi:10.1101/gr.224386.117
...revealed that site-selected editing of protein-coding genes in primates is induced by adjacent inverted Alu repeats or intronic duplex, which function as the recruitment elements for the ADAR enzymes (Daniel et al. 2013, 2014). In this study we found additional editing in the vicinity of pre...
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Research: Tandem repeat variation in human and great ape populations and its impact on gene expression divergence
- Tugce Bilgin Sonay,
- Tiago Carvalho,
- Mark D. Robinson,
- Maja P. Greminger,
- Michael Krützen,
- David Comas,
- Gareth Highnam,
- David Mittelman,
- Andrew Sharp,
- Tomàs Marques-Bonet,
- and Andreas Wagner
Genome Res. November 2015 25: 1591-1599; Published in Advance August 19, 2015, doi:10.1101/gr.190868.115
...but not fixed in other nonhuman primates seem to be enriched for processes related to stimulus detection, sensory perception, and skin development. Such biological processes may be associated with the evolution of human-specific cognitive traits and the response to new environments, respectively. Our results...

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