The birth of a human-specific neural gene by incomplete duplication and gene fusion

Background: Gene innovation by duplication is a fundamental evolutionary process but is difficult to study in humans due to the large size, high sequence identity, and mosaic nature of segmental duplication blocks. The human-specific gene hydrocephalus-inducing 2, HYDIN2, was generated by a 364 kbp duplication of 79 internal exons of the large ciliary gene HYDIN from chromosome 16q22.2 to chromosome 1q21.1. Because the HYDIN2 locus lacks the ancestral promoter and seven terminal exons of the progenitor gene, we sought to characterize transcription at this locus by coupling reverse transcription polymerase chain reaction and long-read sequencing. Results: 5' RACE indicates a transcription start site for HYDIN2 outside of the duplication and we observe fusion transcripts spanning both the 5' and 3' breakpoints. We observe extensive splicing diversity leading to the formation of altered open reading frames (ORFs) that appear to be under relaxed selection. We show that HYDIN2 adopted a new promoter that drives an altered pattern of expression, with highest levels in neural tissues. We estimate that the HYDIN duplication occurred ~3.2 million years ago and find that it is nearly fixed (99.9%) for diploid copy number in contemporary humans. Examination of 73 chromosome 1q21 rearrangement patients reveals that HYDIN2 is deleted or duplicated in most cases. Conclusions: Together, these data support a model of rapid gene innovation by fusion of incomplete segmental duplications, altered tissue expression, and potential subfunctionalization or neofunctionalization of HYDIN2 early in the evolution of the Homo lineage

Genetic effects on gene expression across human tissues

Characterization of the molecular function of the human genome and its variation across individuals is essential for identifying the cellular mechanisms that underlie human genetic traits and diseases. The Genotype-Tissue Expression (GTEx) project aims to characterize variation in gene expression levels across individuals and diverse tissues of the human body, many of which are not easily accessible. Here we describe genetic effects on gene expression levels across 44 human tissues. We find that local genetic variation affects gene expression levels for the majority of genes, and we further identify inter-chromosomal genetic effects for 93 genes and 112 loci. On the basis of the identified genetic effects, we characterize patterns of tissue specificity, compare local and distal effects, and evaluate the functional properties of the genetic effects. We also demonstrate that multi-tissue, multi-individual data can be used to identify genes and pathways affected by human disease-associated variation, enabling a mechanistic interpretation of gene regulation and the genetic basis of diseas

A user's guide to the Encyclopedia of DNA elements (ENCODE)

The mission of the Encyclopedia of DNA Elements (ENCODE) Project is to enable the scientific and medical communities to interpret the human genome sequence and apply it to understand human biology and improve health. The ENCODE Consortium is integrating multiple technologies and approaches in a collective effort to discover and define the functional elements encoded in the human genome, including genes, transcripts, and transcriptional regulatory regions, together with their attendant chromatin states and DNA methylation patterns. In the process, standards to ensure high-quality data have been implemented, and novel algorithms have been developed to facilitate analysis. Data and derived results are made available through a freely accessible database. Here we provide an overview of the project and the resources it is generating and illustrate the application of ENCODE data to interpret the human genome

Genetic effects on gene expression across human tissues

Characterization of the molecular function of the human genome and its variation across individuals is essential for identifying the cellular mechanisms that underlie human genetic traits and diseases. The Genotype-Tissue Expression (GTEx) project aims to characterize variation in gene expression levels across individuals and diverse tissues of the human body, many of which are not easily accessible. Here we describe genetic effects on gene expression levels across 44 human tissues. We find that local genetic variation affects gene expression levels for the majority of genes, and we further identify inter-chromosomal genetic effects for 93 genes and 112 loci. On the basis of the identified genetic effects, we characterize patterns of tissue specificity, compare local and distal effects, and evaluate the functional properties of the genetic effects. We also demonstrate that multi-tissue, multi-individual data can be used to identify genes and pathways affected by human disease-associated variation, enabling a mechanistic interpretation of gene regulation and the genetic basis of disease

Knowing Children: Participant Observation with Minors

When studying children too often it is assumed that our view of the world will be their view of the world. Knowing Children explores this lofty assumption and explodes various myths that researchers commonly hold about children. Using the assumptions that minors are knowledgeable about their world and that the worlds of minors are special and noteworthy, Fine and Sandstrom explore the worlds of children and demonstrate that adults can greatly benefit from studying their worlds through the use of qualitative research methods. In this insightful volume Fine and Sandstrom present timely methodological statements on doing participant observation with children. Drawing on case studies of children from three age groups they provide the first extended treatment of methodological problems with qualitative research involving children which integrates previous writings. They cover general issues involved in research with children, focusing on methodological and ethical concerns as well. This volume provides a fresh view of the worlds of children while providing an invaluable reference for the ethnographic researcher. Knowing Children helps the researcher understand how and why children react to adults doing ethnographic research. This work will prove to be specifically of interest to applied researchers in child development and education. It will also be of interest to those in other human services and more traditional ethnographic fields. [From the publisher]https://digitalcommons.odu.edu/sociology_criminaljustice_books/1035/thumbnail.jp

Symbols, Selves, and Social Reality: A Symbolic Interactionist Approach to Social Psychology and Sociology

The fourth edition of Symbols, Selves, and Social Reality provides students with a succinct, engaging, and affordable introduction to symbolic interactionism--the perspective that social reality is created, negotiated, and changed through the process of social interaction. Focusing on how elements of race and gender affect identity, the authors use real-world examples to discuss the personal significance of symbolic interactionism, its expanding theoretical scope, and its relationship to other prominent perspectives in sociology and social psychology. They skillfully cover empirical research topics that are inherently interesting to students, such as the dynamics of self-development, impression management, identity transformation, gender play, rumor transmission, and collective action. [Amazon.com]https://digitalcommons.odu.edu/sociology_criminaljustice_books/1031/thumbnail.jp