Japan operates a variety of through-services (直通運転, chokutsu-unten) or nori-ire (乗り入れ) or through trains which are direct seamless connections between rail operators, using leased trackage rights and junctions, to cut cross metropolitan area commutes without having to change trains, wait, figure out connections, or cross platforms/stations.
Some far-flung spur lines have been shortened (abandoned stations and track due to low patronage); through service is a frequently used method to integrate the surviving short stub lines into multiple rail operator's systems, enhancing convenience and ridership.
Through-service proliferation is increasingly common phenomenon as the railway networks, urban density (and Japan's demographics) have matured and new line construction is minimal.
There are several dozen unique through service runs in Japan, the actual track usage details are complex (but as a seamless service offers an abstraction layer for the end user), the Japanese Wikipedia page has a complete list.
Standardization is required for cross railway services, in terms of rolling stock dimensions, rail gauge, overhead power, not to mention coordinated scheduling between a mixture of separate companies and/or government agencies.